Mark III primary - tranny oil seal alignment

I'm replacing the seals on the inner primary. Workshop manual says to make sure the tranny shaft is centered in the primary hole. It was low and forward when disassembled and the old seal is worn that way. I have losend the trans bolts and can center it front an rear but there dosen't seem to be enough wiggle room to get it centered top to bottom. Any suggestions, tricks or is that just the way they are?

You have to expand your thinking to include reality. Which is the propensity of very bad mechanics to have previously damaged the engine cases or engine cradle bolt holes. The whole assembly once damaged by running the bike with loose hardware can be small but profound. That is precisely what I suspect.
An undamaged MKIII will align just fine. A larger analysis of the condition of all the adjoining components should be undertaken by a highly competent MKIII commando savy mechanic. Good luck in finding one...A MKIII is a very different bike from a regular commando.