I tried that at the recent spline lube on my R90/6 but there was no combination of re-clutching with loose bolts that reduced the breathing between the transmission and the engine. I couldn't come up with anything to measure the error since it is a really blind assembly. Yes, they will still move around a little but I can usually make them much better. The trick is to have the bolts j-u-s-t loose enough to allow centering but not a lot of breathing shake. Any chance that you have a worn rear main bearing in that bike?
Of course I did not do that on the previous disassembly on the spline strip out as I didn't know a lot about the nature this failure back then in pre-Internet forum days. I do remember though that the input shaft front bearing was also shelled out probably from excessive radial loading. I have seen a number of front bearings trashed when spline damage is present.
You (and anyone for that matter) are welcome to use my fixture for checking Oilhead engine-transmission alignment. It requires the guts to be taken out of the transmission but the measurement can then be made in a few minutes, and includes the indicator. It travels well thru the US post office for only the cost of postage. I also have raw material and a setup to make fairly precise offset alignment pins on my old lathe once the measurement has been made. Thanks for the offer but I have my own as I check every 1150 that I work on for stripped splines (haven't done one I quite a while now though). I have a 4 jaw chuck for my lathe so making offset dowels is fairly easy, just a pain to adjust them to eliminate the run out.