A WAG, OK?
I think this is going to be about the pin at the very bottom of the lower shift shaft, and the "spool" at the front of the prop shaft. That "pin" should be installed so that it's located in the center of that spool. It SOUNDS like it's been installed incorrectly, on one side or the other of that spool, so the spool is moving too far, releasing the balls.
I installed an '06 (I think?) lower on a 2011 90d successfully earlier this season.
I had an issue with it shifting into reverse when it should have been in forward, and forward when it should have been in reverse - opposite of the way it should be. A head scratcher for sure!
The solution turned out to be simple. That pin on the bottom of the shift shaft had been installed incorrectly (by me) when I had it down for new seals and a couple of bearings. It was 180 degrees off, requiring the shaft to be lifted up, then reinstalled so the pin was on the opposite side of the spool. Point being, you're going to need to be paying attention here. Confirm the direction you have it set up for prior to installing it - or risk it shifting opposite of what it should and having to pull it down AGAIN!