I had the same problem with the APE main bearing studs. The two longer ones were not quite long enough.
On my build, I flipped the two longer ones around (so the shorter end was in the case)... this gave me enough thread height on the nut side to have complete thread engagement with the nut.
I somehow convinced myself this was ok
I think I might have looked at the threads on the original bolts and decided the length was about the same as the shorter side, so it should be OK... I don't really remember though... it's possible I'm taking a big risk only having the shorter side in the case.
I don't really need them... my build is just 61mm (1+mm) pistons, but my old bolts were pretty rough and I figured, what the heck the HD ones must be better.
I did 8lbs in the case (even that made me nervous) and 17.5 lbs on the nut (with locktite - so equivalent of 21-22 dry?)
Also, make sure you run a thread restorer/tap on the threads. I found that the longer threads on my APE studs were a little off (it took considerable force to run the thread restorer tap up and down the threads at first). The shorter side threads were fine.
I don't mean to complain... I'm very happy with APE.
APE balanced my crank and back cut my transmission - excellent work and always a pleasure to talk to on the phone (both Jay and his guys had a lot of patience for all my newb questions).