hmmm, yah im thinking that the little shaft that controls those gears might be off abit inside the gear box or might just not be aligned properly with the arm that runs forward from the shifter?
when i did my rx7 gear set swap i had a problem with a leak around the tail housing so all i did was take out the tail housing while it was all still in the truck alot easier and you can check out to the see if anything looks out of places? all the notches should line up nicely in a strait line just make sure you put it in neutral before you pull the shifter out.
and this how they should all look right before installing the tail section back on.