Been having problems with it not wanting to shift into reverse. Shifts smoothly into forward but about 80% of the time it won't go into reverse. When I have to go to reverse, I have to pull the motor out of the water (not running) and turn the prop while shifting the tiller into reverse. Then drop the motor back in the water and go to neutral, start it, and it'll go into reverse like it's supposed to. Then you run down the river or idle a little ways and try to go into reverse and it won't go. Then I have to repeat the process.

Any ideas??

Sounds like a linkage problem. Check all adjustments and linkage rod

I've gone thorough all the linkages. I changed out the carrier bearing in the lower unit since the one that was in it was in rough shape. I'm thinking something in the lower unit is not lining up the go into gear..

Any noise when you try to go into reverse?

Nope, no noise at all.