I recently took my lower unit off checking for a leak. I had it in reverse when I removed it. When I put it back together it would not go together. I tried turning the prop but that didn't work. I finally slowly moved the throttle towards neutral and it popped into place. When I took it out it was hard to put into gear. The motor sounded rough, and I couldn't get it up to speed. I killed the motor, restarted it, slammed it forward, stomped on the hot foot and it jumped out of the hole and ran well. It is still hard to shift and dies when I put it in neutral. I have a 2009 225hp yamaha vmax.

take it back off, your shifter shaft is one notch off most likely. Move the shifter shaft on lower unit back and forth until you find where neutral is on it. Leave it in neutral. Place shifter in neutral. reinstall. may have to move the
shifter very slightly or the main drive shaft slightly (like 1 or 2 degrees) if it does not go at first. Trail and error at that point. Wire brush and grease everything well first.

So keep throttle in neutral and remove lower unit and take some pliers and turn the shifter shaft a hair to left or right and slap it back together?