Now that I'm back home, I have a chance to measure a few things out:
The shims (2) are each .25mm thick. Of the washers (3), the thick one is 2mm, the thin one is .5mm, and the wave washer is 1.25mm.
So that the wave washer does not act upon soft aluminum on either side, it surely must go between the trunnion and a washer. Even though the machined face of the trunnion is not as wide as the wave washer, I suppose it's adequate.
Using the diagram as a guide, I assembled left support (1), thin washer, wave washer, then trunnion. On the right side, support, thick washer, then trunnion. The action of the wave washer makes the spacing on that side 1.3mm larger than the opposite. I manipulated the transmission through the gears without problem. I then swapped sides with the washers; 1.3mm larger spacing now on the right. Once again, I manipulated the transmission through the gears without problem.
Unlike how I found my trans during disassembly, I now think the thin/wave washer combination go together in the above-mentioned order; which side seems immaterial. I reassembled the components with the two washers on the left side, as seen in the diagram. If for some reason I need to revisit the construct, I can readily access these components from inside the car, without dropping the trans again.
The whole arrangement does not compress the wave washer that much. It makes me think the situation is less about centering, and more about maintaining friction in the gearshift lever for tactile feedback. Even if I put all the shims on one side (which they certainly were not), it would only move the centering of the gearshift lever by .5mm.