Jamison, yes. There actually appear to be THREE bolt patterns:
* Small holes, small diameter bolt circle.
* Large holes, small diameter bolt circle.
* Large holes, large diamter bolt-circle.
If the holes all line up but the bolts won't go through, just get the drill out. Trust me, though, if you have to drill 4 NEW holes in the flange, it's MUCH easier to get out the 30MM socket and breaker bar/impact and take the flange off, and drill in in a vice or with a drill press.
I did the first hole at the front t-case output flange with a hand drill. My arms were sore by the time it was done, so I yanked it off and did the other three in a drill-press in the time it took me to do the first one alone.
Be sure to stake the nut down real good with a punch and hammer when you put the flange back on.
