Jon, Gary et al
No need to worry about how good or bad the flanges happen to align. Welding by its very nature will cause these slight variations. The important thing is to make sure the bearing blocks are all in alignment. I used a copper pipe as a guide to get the bearings straight. After that almost anything with good compressive strength can be used as a filler to take up the unevenness between the flanges. I used aluminum spacers. If the holes happen to not align, simply drill them out.
Chris
Chris Zavatson
N91CZ
360std