Yahoo, it's in! I did end up pulling the motor back out of the truck and re-aligning the clutch so that the alignment tool came out easily. I'm not sure if this did the trick, or if I just managed to hold my tongue right while yanking, lifting, shoving, kicking, etc. the motor into place. This time it fell in with about 3/16" even gap between motor and bell housing. Put the bottom 2 bolts in and the gap pulled closed without resistance - yay!
Now, just have to finish bolting it in and then put all the accessories back on. But I'm stoked - I won this 2 hour wrassling match this time around!