Hi Bob,
The inner case is easily distorted an so may have taken a "set"
"Normally" the only way the crank nut can foul the outer case is if the nut comes loose
(plenty of posts here on this topic
)
If the inner case is too far out from the engine / gearbox the first thing to foul will be the primary chain on the inner case
I adjust the distance from the engine /gearbox by adding or removing gaskets or a thinner spacer as required
The "variable" is usually the clutch centre taper and no way of really altering this except to try different ones
I then align the engine sprocket to the clutch chainwheel, shimming or machining as necessary
Then strip the clutch off and fit the inner case loosely, refit the clutch centre and move the inner case onto the scroll and do a rough measure as to what spacers /gaskets are needed
Add the gaskets and spacers and refit the inner case and centre and check that it is all free to rotate
Alter spacers/gaskets if needed, then assemble clutch and primary chain and keep checking that all is ok as you go
Yes, check front screw length before final fitment, remembering that the crank's closeness to the case changes with the crank position
HTH
John