Is there some reason you can't remove the engine from the frame? The job you're contemplating isn't a weekend project. It would best be done with at least a partially disassembled engine- - - -a bare block with nothing but the crankshaft in it would be the best approach. I've got a couple of bare blocks and several bell housings out in the shop- - - - -in the next few days I'll look at the alignment dowels and figure out how the factory did it. Probably the best bet would be to make some offset dowels and clock them for the minimum runout.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
Cringe and wail in fear, Eloi- - - - -we Morlocks are on the hunt!
There is nothing noble in being superior to your fellow man; true nobility is being superior to your former self. - Ernest Hemingway
Love your enemies and drive 'em nuts!