I just changed out my lower unit and when I got everything hooked back up, I noticed that it won't shift into reverse.  I get forward and neutral just fine.  It was shifting fine before I changed the lower unit.  For some reason, I was able to shift it into reverse a couple of times, but then when I shifted forward again, it wouldn't go back into reverse.  The shifter won't budge into reverse once it gets past neutral.  I didn't change anything except the lower unit.  Any ideas?

I would say that the shift rod needs to be adjusted.  What type of motor do you have?

It's a 1990 Suzuki DT85.

I did notice that before I put the replacment lower unit on, the shift rod took a lot more effort to move up and down than the rod on my old lower unit.  It was especially hard to pull the shift rod up.  I believe that "up" is reverse.  Does that help?

OK, so I did some more messing around with it. I fired it up in the driveway and with the motor running, I can get it into reverse, although the shifter feels a little stiff. Prop engages in forward and reverse and is not spinning in neutral. When I went from forward to reverse with the prop still spinning a bit, it did grind louder than what seems normal. When I shut the motor off, I got it into reverse once, then back to forward and when I shifted back to reverse, it wouldn't budge again. What's the deal? How can I get reverse with the motor running but not get it when the motor's off? Please help.

It could just be the way the clutchdog is lining up the gears to the pinion. Have someone slowly spin the prop by hand as you shift into reverse. It should go into gear and stop spinning. It should go smoothly and quietly. If not have a mechanic take a look at it.