Those dowels are there to align the timing mark with the #1 and #6 cylinder top dead center. As long as the bolt holes align, a flywheel could be installed without dowels at all as long as the bolts are a tight fit in the flywheel holes, or just one dowel could be used if you're willing to re-mark TDC on the flywheel. Be sure to plug the unused dowel holes to prevent possible oil leaks. I'm not sure if the dowel holes go all the way through to the crankcase- - - -but I'm sure the bolt holes do. I lost a clutch from oil contamination shortly after purchasing a 59 3800 with a "rebuilt" 235 because the PO left a flywheel bolt out after cross-threading it.
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!