I was thinking of maybe spacing the rear mount of the gearbox by a few MM's to give me some clearance at this point as mine only has about 1-2mm static and you can see evidence of contact in use. I can't see that the diff to propshaft or diff to G/box angle would cause a problem here as the minute angle change would be taken up by the U-J's and sliding joint. I don't think you could even measure the angle difference it would create and when you look at the chassis itself and the crossmember's accuracy I'm sure they all vary slightly in position. Yet all the rear mount spacers will no doubt be the same! As a last addition, the cross member shows no damage or deviation in it's construction or fitting no do the chassis rails which are straight and true.
Again any thoughts would be gratefully received. I have been an automotive R+D engineer for my sins but I don't think you can really apply any construction and use regs to a Morgan chassis, well not within any real tollerances anyway!
Thinking out loud re spacing the rear mount….

Probably worth a bit of experimentation first. There’s a bit of an unknown situation on the top side of the gearbox, as there’s no visibility. Depending on the space available, any critical clearances between the top of the box and the underside of the gearbox cover/tunnel could become compromised? Also as you would be pivoting on the front engine mounts, you would need to raise the rear roughly double the height of any additional midpoint clearance required at the guard (depending on the geometry).