Eric,
Sounds like the oil pump and the spray tree/bar is o.k. However if the center web of the crank does not have the shallow grooves, the oil is not going to be able to get into the connecting rod bearings as it ought to.
You will need to be more specific about the clearance in the 'middle' bearing. Is the play in the bearing itself, that is between the inner and outer race? Or is the play in the fit between the bearing and the journal of the crankshaft? Either way, it needs more investigation as it sound like something is amiss.
The long timing side shaft, apparent lack of oil grooves on the center web, and mention of a 'middle bearing' (implying there are three) make me think you have a 1935 crankshaft in a 1936 engine. Have a look again at the photo I posted of my 1936 crankshaft. Note the timing side shaft is short. It ends at the nut for the timing pinon.
Also it contains the answer to your question about crank pin bolt retention. There are supposed to be a tab washer under the bolt head.

1. Marks of the heads of the tappet adjuster from the tip of the valve stem. Normal.
2. Make a new washer, but keep the outer diameter smaller than the root of the gear teeth. The spare list does not say how thick the washer should be. So copy what you have, or try to figure out what the optimal thickness would be to bring the face of the pinion flush with the rest of the gear train.
3. See above.
4. Simplest answer is that piston (and rings) were passing more oil than the other. Be it scoring in the cylinder, rings tired, excessive ring gap, ring flutter, or all the many things that lead to excessive amounts of oil getting past. De-coking engines was a fairly regular ritual back in the day. We are rather spoilt by modern engine in comparison with better air filtration, lack of dusty roads, and lower mileage on vintage machinery as to expect never to do need to scrape carbon. Having said that, both pistons should carbon up at about the same rate.
5. Yes.
6. The aluminum seems to have been 'smoothed-off' at the factory. Or at least in the areas where readily accessible; they did no go into every nook and cranny. Nor did they bother on areas not readily visible, such as underneath. I don't think it was polished to a mirror reflection, more of a satin finish. Most likely it was a job given to the apprentices, so the amount and diligence likely varied from motorcycle to motorcycle. As previously mentioned and shown in the adverts, much of the timing side face of the engine was painted black.
-Doug