01 Integra LS

When I got the car everything was apart and in the trunk.. This is my first major overhaul.. Now Ive got the tranny, engine and stuff back together and mounted in the car.

MY PROBLEM..

I get everything out of my way, but when I go to connect the axle to the tranny it doesnt go all the way in. there is about a 1/2 inch between the hub/boot and the tranaxle case. after a little bit of turning and pushing. it still wont sit flush.. I back up, take a look through hole where the axle gear shaft goes(the 1 1/2 inch hole on the bottom back end of the tranny) and i notice a bar that goes right through the middle of the holes path.. I stuck my finger in there and it seems to be cylinder shaped, roughly the size of a sharpy in diamiter..

How the heck do I get these axles connected?

Thanks TR.
No worries...