If the gearbox bottom mounts and cross stud all line up fine, the lower frame members are OK. Could be the frame was made that way and there is enough flex in it to line up that top mount. Cross support between plunger forgings and a car jack should do it. But this is not how it should be, frames under tension are a bad thing. When assembling frames and engines it is always easier to have everything loose so parts can move and settle get every fixing in place and then tighten.
If the frame fella's check is OK, the easiest fix is to add material to that gearbox top lug and redrill to match. But before anything is done it may be worth checking that the mudguard, air box and oiltank fit. If not this is a pointer towards something further amiss with the frame.
I'm sure somewhere there is reference to a shim type gasket sometimes fitted between the gearbox mounting face and the crankcase. I reckon this was a factory dodge to keep the mainshaft concentric with the seal on examples of over enthusiastic machining. So RD has a point, and another gearbox shell for comparison would certainly help to sort this conundrum.
Swarfy.
