Gen 5 transmission

Hey all, so somehow I broke my output shaft while riding the other day. So ordered a new transmission, installed it and now it’s acting up on me. For some reason it won’t go past 3rd, shift lever is pretty squishy at 3rd. I’ve took out in out in the tranny multiple times now making sure everything is aligned and in is installed in neutral. Anyone have any ideas what’s going on?
thanks