Man, I doubt it. The shifter arm is made of steel. The shift fork down on 5th/rev collar is aluminum, but if it worked before, I doubt it is screwed up now. You are for sure getting the steel shift lug on the inside of the driver's side of the case lined up with the corresponding component on the cover?? If you are having issues with it, it may not be in neutral. IIRC, the 5th/rev can be "over-shifted" to actually go past where is should be limited to so it feels like there is an extra detent beyond the normal range of operation. I'm not sure if this can happen with the rear housing on, but I think I experienced it when it was off. That is all I can figure it can be. It is a bit tricky, but with all shift collars in neutral and a little screwing around with that 5th/rev steel arm the cover should drop on with no force required to seat it.
Hope it helps.