Sorry for all the extra work you had to do, but (like all of us here, I suppose
one becomes an A expert by owing and riding one, redoing things a few times is what gives expertise.
Have never heard, read, or seen the gearbox problem you have, may have originally started due to a crash or shock, then the tension of the bolt + vibrations\movement made it worse 'til it cracked. Welding aluminium is a skill, did they weld the part back on? If so, better to forget the cracked piece, and rebuild the whole with aluminium welding. Needs a good man to get the rebuilding right. Then drill out, file and polish etc until it gets the original shape. Then chech that the frame is completely flat against the gearbox surface, eventually straighten, file\polish or whatever till it is, use a correct diameter bolt then use a selflocking nut and do not tighten more than neccessary.
Your new gearbox housing may be 100% fine, but still do a check for 100% parralellness (is that the word) to the frame at the contact point and use a selflocking (or loctite it) with just enough tightening, then check all other engine\gearbox mounting bolts, if something is moving the stress may end up at the point where you got the cracks. Just some toughts that emerged, hope some of it may be of help, good luck.