I thought the same thing when I did mine last week. I ended up just getting it in there far enough so that the cover with the 3 tabs on it would hold it in, and would still allow the valve body to be bolted up. Mine shifts fine, so I assume that this is correct. Not a tranny expert, but I'm sure that if the way I did it was wrong, that the 2-3 shift would be acting funny, or not doing anything at all. I'm sure someone w/ more knowledge will comment.
These are highly engineered precision vehicles, the first step in diagnosing the problem is to strike the suspected offending part sharply and repeatedly with a blunt object, then re-test.