I just want to put this thing in once and have it run properly so I figured I would ask.
In this case check the following with a dial indicator which can also help with troubleshooting if needed:
1.Mount dial to bell housing with stylus touching where the clutch disc contacts the flywheel. Rotate and look for axial run out. If refaced check again after that process.
2. Mount dial to crank and/or flywheel with stylus touching transmission mounting hole in bell housing. Rotate and look for radial run out between transmission input and pilot bushing.
These procedures are covered in the shop manuals which will also state the allowable run out tolerances. Personally I want those numbers under .002” and will make corrections to obtain it. Both the crank and bell housing are dowelled so it should be close.