Hi,
Interesting problems. I'm not experienced with the S6 engine, so treat the following as general advice. No doubt I'll be corrected if I get it wrong.
If the timing side bush is as designed, it was a bad design. Mostly the bush here would be a "top hat" design, with a flange inside the crankcase. The flywheels would normally bear against the flange of the bush, and the thickness of the flange determines the alignment and end float of the crank. You can't (ok, you can but you shouldn't!) put a shim on the timing side between the flywheel and the bush. Shims should never go between parts that rotate relative to each other.
Because the engine is now really old, all manner of things may have happened to it over the years. The best you can do is to put it right as best you can.
1. Make sure the con rods are straight - not bent or twisted. The human eye is very useful if you don't want to dismantle the crank.
2. Make sure the main shafts are round, particularly the timing side where it runs in the bush. Wear here can be pretty bad.
3. Put the crank in the cases with the two races and the current timing bush is place, and no shims anywhere. Presumably there is a thin paper gasket between the crank case halves?
4. The crank should be a sliding fit in the inners of the ball races, and free with little measureable play in the timing side bush. Check for end float. I hope there is lots - maybe a mm or two.
5. Measure as accurately as you can the centrality of the rods in each cylinder opening.
6. Hopefully there is enough end float, and the alignment is such that the timing side bush can be replaced with a top hat design, with a flange thickness chosen to give a little end float (0.010"/0.25mm or so). When you make a new bush, remember to chamfer the inner diameter where it bears on the flywheels so it doesn't bind. Pay attention to oil holes and distribution channels.
7. The two-ball-race setup on the drive side is fine. If you need to shim, do it between the cases and the bearing outer. Make sure your races have appropriate clearances: they are probably interference fit in the cases (heat cases to put them in and take them out) and sliding fit on the main shaft, so 00 fit is probably OK - your bearing man will know.
Good luck,
Leon