I know it's done now, but I'll just add this in case anyone uses this post for future reference.
You can sometimes end up with the dowel in the bell housing matching a dowel on the engine, so just remove one of them, otherwise you'll be almost in and wonder why it won't budge the last 5mm.
X2 Yes i have had this once in a life time was enough[bigsad]
The time that occurred i was swapping a RRC 3.5 out for a 4.4 .
So really it should not be a problem with the orig motor and box going back in[bighmmm]