Flywheel hits the gearbox? Two possible causes spring to mind:
* Flywheel is spaced rearward
* Gearbox is coming too far forward.

Yes the flange adapter must come off to replaced the rear seal. So maybe the gearbox flange has been shaved by a previous owner, in order to "solve" a clutch adjustment problem? Crazy, but ...

Might as well pull it out and get it fixed.

Sorted it out today. You were right on all the points dd as usual 😜

My problem turned out to be that someone had modified the clutch fork pivot point. Moving it out approx 10mm. This was probably to compensate for having a short bearing carrier and engine plate installed at some point.

Now I tried to fit the gearbox without engine plate installed the end of the clutch fork at the pivot end was actually jamming against the clutch pressure plate stopping engine rotation!

Because I didnt have the engine plate I simply removed the spacer they used to move the pivot outward and put it all back together. Running fine now