EFI Distributor: Length of shaft matter?

first off unless you have also upgraded to a roller cam from a 5.0 the distributor gear will chew your cam to bits. you need to change the gear to cast iron gear instead of the steel gear on it already. you need to find the correct gear because the shaft diameter is also different between the stock points style distributor and the efi/roller cam distributor. this is most likely the entire problem that you are having.

The longer EFI unit should go in, unless you have an aftermarket oil pump drive for a points distributor. If it's the original pump drive, the slip collar might be keeping it from going all the way down, otherwise the shaft should fit over the pump drive, as it's the same size all the way down to the pump. A heavy duty drive is larger past the hex ends and the ones for the later , longer shaft distributors have a longer hex end for this. I also agree with bnickle's advice about the roller dist gear. If you've got a flat tappet cam, and a roller dist. you need to swap gears.