I had a very long written description of how to check a Mark series crankshaft, on the assumption that one of the crankpin press fits had slipped. This is not an unheard of fault. But then I re-read your post more carefully, particularly the part about the center web looking twisted. This is bad, really bad. If it looks twisted, it probably is. A way to check this more accurately than just by sighting it is to place an adjustable parallel between the center web and the adjacent counterweight as shown in the photo below. If you do not have an adjustable parallel, use any block to fill the space to within the range of your feeler gage set. Unless a rod breaks and wreaks damage, the counterweight face usually can be relied on to stay square to the main shaft, and so be used as a datum to measure if the center web has been twisted.

The test suggested in the Mark series handbook of being able to pass a gudgeon pin through the small end bush of both connecting rods simultaneously has its limitations. Definitely there is something wrong if it fails this test. But you know not if it has bent a rod(s), sprung crankshaft, or both. If one or more crankpins slipped slightly but otherwise the crankshaft or the rods were not bent, you could still pass the gudgeon pin test as the crankpins are out of plane yet still parallel.
If the center web is twisted, then the crankshaft is going to have to come apart. While it might be possible to make tooling to get a purchase on the center web to try and twist it back, trying to discern between the influence of twist and slip by measuring the eccentricity of the main shafts is going to be impossible. Also any trauma to the crankshaft sufficient to twist the center web probably has in fact bent the rods slightly. The only way to properly check those for alignment is when they are dismantled from the crankshaft. A method for checking the connecting rods is outlined
here.Even with the center web separate from the crankshaft, it is not going to be an easy task to twist it back to the requisite accuracy, and have it flat too. It might be simpler to find another crankshaft and use the components from that or have a new center web made.
But this is fraught with problems too, as there several different crankshafts, and the parts do not mix and match. Early cranks fed the lubrication oil through the hollow front crankpin to the center web first, and from there it was distributed to the sides of big end bearings. The rear crankpin was also hollow, but it played no part in the lubrication circuit. Later crankshafts had small holes in the crankpin that lubricated the big end rollers directly. However the rear crankpin only gets what oil is surplus to oiling the front crankpin and this is felt to be a retrograde. Then there are crankshafts stamped X004 on the counterweights. These are crankshafts refurbished by the Works with 0.004” oversize crankpins.

Even with the same design components, some have reported an inability to get the crank to run true enough; which suggests components are not as interchangeable as one would like.
A preliminary check for just crankpin slip can be done by pushing a 5/8 pin through the hole in the counterweight and visually sighting how well it aligns with the bung in the adjacent crankpin.
Typically removal of crankpin bungs is to press them right through the crankpin. This should only be done after the crank has been separated, and not while the crankpins and connecting rods are in-situ. The reason for this is the hollow crankpins are a centrifugal trap to collect sludge; which during the process of pressing out the bungs will be extruded out the crankpin oil hole and into the big end bearing. If the big end bearings feel good and you do not intend to disassemble the crank- just clean it- extruding all this filth into the bearings creates a contamination impossible to flush out properly. Also some will be pushed back into the oil gallery drillings in the crankshaft, perhaps blocking them off. However some bungs are not just individual plugs in each end. There are (of course) many varieties. Some are steel pins that run right trough the crankpin, with a reduced diameter section in the middle to create an annular void. Others just have a flat milled on them to allow the oil through. The problem with all of this is you really do not know what type you have till you take it apart.
Far as I know, the factory used a mild steel bung; bungs made of aluminum indicate a subsequent rebuild (I could be wrong on this.) And if these are pressed in too tight, the soft alloy tends to get shaved on insertion and subsequently fall out. Usually on the way to the sump they jam between the counterweights and the connecting rod, bending the latter. The engine will continue to run (for a while) but feel as if it is down on horsepower. As the rollers develop flats, the engine takes on a harsh feel as if the magneto is overly advanced. You don’t want to ask how I know all this.
I have heard some folks replacing the soft bung with a hardened steel bung, inserted with a heavy press fit to expand the end of the crankpin and so make it a tighter fit in the throw. Apparently some light-weight Villers engines used this method. I have never tried it myself to see if it indeed is capable of expanding the pin or not. However, since the normal method of removing the bung is to press it right out through the other side of the crankpin you are setting someone else up for a sore trial in future when they go to un-do your work.
The truing stand you made up is one of two methods the enthusiast can create to check the concentricity of the crank main shafts. It is the simpler of the two, and indeed the one you have to use if the centers in the ends of the main shaft are damaged or otherwise not reliable for setting up to. The precision of the v-notches in the fixture are really not as critical as you might first think. They do not need be precisely the same size, angle, depth, nor perfectly aligned. There are some caveats to using this method that need to be understood else you could get erroneous results. The main journals where they ride in the v-notches have to be round. If the main shafts are worn eccentric, the main shafts will rise and fall in the v-notches giving the false indication the shaft is bent. Typically the front main journal is the one that has to be watched, as the rear is pressed into a ball race.
Second, you should keep the width of contact between the journal and the v-notch as narrow as practical. If the crankshaft were perfectly true, it would not matter at all; the cylindrical journals would lie nicely in the bottom of the v-notches and spin about the shaft axis. But we are checking a bent shaft, so the cylindrical journal lies at an angle through the v-notches. It will rise and fall as it rolls about the v-notch, once again throwing a bit of error into the observed measurements. So if the fixture is made out of thick material for rigidity, cut back the face of the v-notch to make it narrow. This will minimize the effect of the eccentricity. If the fixture is just plain soft steel, a 1/16” to 3/32” wide surface and a smear of lubricating oil should be enough to keep it happy. If it were hardened it could be narrower yet, but the risk here is wearing a score in the main shaft and also an increased sensitivity to nicks and dents (imperfections) in the surface of the journal that will cause permutations in the indicator reading. The illustration below shows one v-notch in place and another adjacent where the chamfers can be more clearly seen.

Lastly, the v-notches should be as close to the throws as possible without riding up on the radius (fillet) ground between the main shafts and the throws. This is important if you are also indicating the truth of the crankshaft on the main bearing journals; you want the indicator stylus and the v-notch as far from each other as possible to increase sensitivity. If you are indicating out at the ends of the shafts and trust them to be concentric to the main bearing journals (and they ought to be, but you have to verify it) then having the v-notches up against the throws is not so critical. In either case, you should setup some sort of end stop to lightly push the crank against while you rotate it, so that it does not slide back and forth axially. Particularly so if you are indicating on the flywheel taper! You could use the chamfers to keep clear of the bearing radius; the face of the v-notch could serve as the end stop.
The other method of checking the crank for truth is to spin it about the centers in the ends of the main shafts. Either in a dedicated flywheel truing-stand in a metal working lathe. If using a metal working lathe use a dead center rather than a live center in the tailstock. The bearings in live centers (unless of high quality) tend to have a slight bit of run out, and you really do not need the high thrust capacity of a live center. To use this method the centers in the end of the main shafts need be in good condition and concentric to the shaft. Often they have been damaged by hammering on the ends of the shaft to drive the crank through the bearings, particularly the flywheel end. Thus when the center is introduced, it is not on the axis of the shaft and when the shaft is rotated that axis revolves about the center and not concentric to it. Therefore it could appear the crank is not true, when there is nothing wrong with the alignment of the throws.
But given the centers are good, this method has an advantage over the v-notch fixture. You indicate directly on the main bearing journals and you have a direct reading as to how much it is out and which way. With the v-notch the ends of the shaft are out in the opposite direction to which the main journals need to be moved to restore truth, not quite as intuitive. If both throws are twisted the same way it shows up clearly as the ‘high’ spots as indicated appear to be on the same side. If both throws are twisted in opposite directions, the high spots are at 180º to each other. If one side is twisted a little more than the other, that side will have a proportionately greater indicated error, and the high spot will something other than 180º, indicating the bias of the error.
There are Ø0.626” holes reamed through the counterweights, they provide a fair guide to assembling the crankshaft. By using a precision ground 5/8” rod, passed through the hollow crankpin and the hole in the opposing counterweight, the crank can be pressed back together with the assistance of this alignment. Absolute alignment should always be done by checking the main shafts for run out with an indicator.

Final adjustments do involve a hammer. The old method of truing V-twin disk flywheels was to thump one or the other disk down on the top of a stout wooden workbench and let the weight of the flywheel do the work! You will hear this method referred to as “bumping”. But the Mark crankshaft does not have enough inertia for this to work. It does not require a hand sledge; just a 1.5-2 lb hammer is enough with a smart tap to the shoulder of the counter weight that you want to shift. You need to contrive a way to hold onto the center web in a stout bench vice. This can be difficult as one with enough of a throat to hold the crankshaft often has jaws of such depth as to foul the big end eye of the connecting rod. Narrow shims might be required. Do not hit the crankshaft directly with the hammer, use a 4” length of aluminum bar about Ø3/4” as a punch to prevent marking the crankshaft. Use something that will transmit the shock of the blow without marking the steel. You might think of using a lead hammer or a hard plastic hammer or a ‘dead blow’ filled with lead shot as being kinder and more persuasive, but these do not work. These are too soft and too much of the impact of the blow is absorbed. With a dozen smart blows I was able to shift a crankpin on a scrap crankshaft that had slipped. (See image below.) I was not able to get it to budge at all using a dead blow or a lead hammer with three times the mass no matter how hard I could feasibly strike it.

So you get the crank pressed together, (leave 0.010” end float for the connecting rod.) and then check it. You then give one or the other counterweight a good clout which ever way you have determined it needs to go. Then you check it. Then you clout it again, harder if it did not move. Then you check it again. And so on, ad-infinitum. You need to keep checking to see if it is moving at all and to adjust the force of your blows accordingly. If the indicated run out gets better, you are headed in the right direction. Diminish the force of the blows as you ‘sneak up’ on zero so as not to overshoot the mark. If the indicated reading then starts to get worse without ever reaching zero, and you are sure you have not overshot the mark, then you need to start adjusting the other crankpin. Remember only work on one at a time. Do not jump back and forth between the front and rear crankpin at random but be methodical. Get as close to zero as you can with one end, then switch to the other. When you have done all you can there, switch back again. It is a trial of diminishing returns and if it sounds tedious, that only just barely describes the frustration of the actual process. This is where the beer comes in, as it can lubricate the process. But in moderation, you are wielding a hammer after all!
If you just had slipped crankpin, then you could have trued up the crankshaft without ever pulling it apart. It is likely that just one of the four crankpin press fit interfaces slipped, or just one crankpin. If one is a little less of a press fit than the others it stands to reason it will slip first. So if you can determine which one it is, you can concentrate your corrective efforts there and avoid some of the trial and error approach. If not, alternately clout one throw then the other, with increasingly heavy blows, till one slips. This is likely the one that gave way in the first place and you should start your corrective actions on that one and see where the measurements lead you. The bad news is this: it will probably slip again in use as the underlying fault is an insufficient press fit. Bump starting the motorcycle really is no different than driving the crank with the kick-starter. Unless you were towing the bike at a high rate and were able to suddenly engage the clutch, the clutch had no slip, and there was some unusual resistance to the engine turning over, it seems unlikely that on its own the crankshaft should have twisted unless one of the press fits was insufficient.
The crankpins are assembled with quite a heavy interference fit, and it pretty much requires hydraulics to get them apart and back together. The throws do not take kindly to being pressed apart and together too often, and they stretch. (Remember the 0.004” oversize crankpins?) This is even more likely if your press does not keep all the components nice and square and tries to push the crankpins in crooked.
As for concentricity “how close is close enough?” At worst you should not accept an indicator reading of total run-out greater than 0.0015” anywhere along the shaft. Otherwise life will be hard for the main bearings and their life foreshortened. Also depending on how tight the rod bearings are, the pistons could be presented to the cylinder bore crooked, increasing friction and risking seizure. If you can get it between 0.0008” and 0.0010”, you can call it quits and consider the job done. Obviously if you have the patience to get it closer than that, then that is even better yet.
If the crank jammed in the front bronze bush you might need to renew that as well. Do not make it too close a running fit or they tend to seize and spin in the crankcase, cutting off all the oil supply. If it has too much clearance the oil just leaks out, so starving the crankshaft for oil. Damned if you do and amend if you don’t.
-Doug
[missing hyper link added 23oct07 -Doug]