The adjustments do not actually affect the overall position of pump timing to engine. The fuction is to keep all the pump elements sequentially putting out the fuel of each injector at the exact right time in comparison to the other elements of the pump. If one is not where it should be that engine cylinder gets its injector spray a little earlier or later than the engine designer intended compared to the other pump elements outputs. At this point do not get particularily concerned about it. You can fix that if it turns out to be required. Of course at higher engine speeds the basic problem will not be as noticable the fuel does not have enough time to get back through the leaky return valve because it just has much less time between element pump strokes as the leakage rate is the same but time is much shorter. This is not rocket science if you slow down and think about it. You can either do the output volume test to make sure it is this type of problem. (not enough fuel in comparison to another element). Or just try a good crud dissolver might solve the problem without the need for test and repair. I do not have a clue why the shims are there but suspect they might be to alter the size or volume of the pump chamber. Simular effect to adding a thicker or thinner head gasket but as I said do not have a clue. My other pump stuff is just basic common sense once you know how the pump basically operates. For example I have no knowledge how the pump is internally controlled to provide more or less fuel to the injectors other than they must vary the pressure by pump cylinder volume I imagine. That would allow a longer period of high pump element pressure allowing more fuel to be injected with each stroke as the injector is open longer but again not certain. Do not even want to think about how they advance the timing internally either. I think I just figured a way they might get the mechanical timing advance as I was typing my last sentence. Higher pressure for a longer time span means the injector would be forced to open earlier to get the increased amount fuel in. Really a pump is a pretty exotic kind of mechanical engineering. Probably gave the original designers ulcers or worse during it's initial development.