Those dowels are offset slightly so the flywheel will only fit in one position. The bolt holes are evenly spaced. It looks like you failed to align all the dowels before you tightened the bolts. If the dowels can be drilled and tapped for a thread, you might be able to install a stud into the ones that are pushed inward, and use a socket over the stud and a nut to retract them. You will probably need to have a machinist make some new dowels once that's done, since a dowel with a hole in it will allow oil to leak- - - -the holes go all the way through the crankshaft hub. Ditto for the bolt holes.

If the dowels are too hard to drill and tap, good luck!
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!