Can i add shims to the transmission shaft to the crankshaft or flywheel to get a good run out?
In my experience, yes.
1. Ensure the mating surfaces are smooth and free of any burrs etc.
2. The transmission shaft can go on in one of two ways (180° apart). Find out which orientation results in the least runout and, with that as a starting point, shim from there (under the trans shaft flange at the point of greatest run-out). Usually a 0.001 or 0.002 shim around, say, 120° of the circle will suffice.
3. Same procedure applies with the flywheel — can go on in one of two ways, choose the closest and go from there with a shim under the side of greatest runout. To clarify, this is not axial runout around the perimeter, but more like flutter as when a dinner plate is spinning down to flat.
I can get the trans shaft to within 0.001-0.0015 total runout and flywheel to maximum 0.002 flutter with this technique.
Better to machine the transmission shaft flange to remove run out or find a straight transmission shaft. I have also machined the crankshaft flange to remove run out.