To be open, I never liked the original design of bolting down the lot to the engine case. Even less the B-Rapides two part bolts. All components should be a good fit as they are parts of the chassis , no frame here on the bike. The not so great way of positioning is the long fit of bolts in the through holes so you have to pull the lot all along the bolts for disassembly and same when mounting all. It is common practice since a long time to have hollow dowels like in engine cases for cylinders and heads as well. Just 1/4 " depth bores - or 5-6 mm - for short bushes , 2 thou max slop , and all components will fit nicely, from top to bottom.
Certainly this is a job for the mill and DRO fitted but later you just have simple 10 mm studs , I had 10 x 1.5 mm standard thread in alu adapters in the case and 10x1 mm fine thread on head brackets. All stainless bolts, do my own tread rolling in seconds, without having easy machining stainless. No eight nuts per head for mounting head plus bracket, questionable practice in my eyes,so a no-no for me.
Vic