5th gear pop/clunk on 89 spg

I changed the trans in my 1989 saab 900 spg over a year ago, with a trans from a 1988. The primaries have been moved from the original spg trans to the 1988 trans. I really haven't had much of an opportunity to drive the car except around the block a couple of times. I found that going into 5th was a little bit of a problem. It will go in, but you have to hold it there in place and then it will "Pop"! with a bit of a clunk into 5th. Im not sure if this is an alignment problem or a trans problem.
When I first aligned it, it would go into all gears except 5th or it would go into all gears except reverse. I managed to get it to go into both, 5th and reverse, but again, it isn't smooth, there is a pop/clunk going into gear.
Any ideas?