In regards to the issue of the crank-pin nut contacting the bearing liner screw......

I've had a word with the JAP Guru... and his advice was to simply take an angle-grinder to the crank-nut and
make clearance!

Apparantly it's a common thing, the cases are "not" exactly precision made, and there's a lot that were cast by jobbing engineering firms after JAP stopped production, so exact fitting is not always going to happen. His advice was to figure out the desired shims on the crank (to get the piston and con-rod as central as possible), then see if the nut is striking the liner screw (and the casing), and then get the grinder out!
He also suggested that if I wanted to confirm the clearance I've created, I can fit slightly narrower shims (eg ten-thou thinner), and see if there's contact. If not, then I should be good for the lifetime of the engine. Sounds like a plan to me.

He also pointed out; when I mentioned my concern about affecting the overall balance of the crank; that shaving a 1/16th off 1/3rd of the crank nut would be akin to taking a piss before a weigh-in... totally irrelevant!

Which was reassuring.

So - that'll be the next thing on the list! GRINDING!