problem with lower unite F150

Well I thought I would change out the empeller on my Yamaha F150 . Thought it would go pretty ez . Well, I had a problem with getting the lower unite back up , it wouldn't go all the way up against the mid section. Thought if I could get a bolt in I could jack it up the rest of the way . That worked, thought the intake tube was sticking . When I started the engine I heard a clanging , both in forward and reverse . I dropped the lower unite down and it looked like the shift lingage didn't mate up , so I played with that while the lower unite went up with no problem .
Started the engine , same problem . Sounds like somethings banging and at times it'll start shuttering . It does this in both forward and reverse .
Everybody have any ideas ? Thanks in advance . Pat

Well I guess I'll anwer my own question. The speedo pick up didn't line up right, must have tilted a bit. I didn't go up into the mid section fully, causing the shift spline to slip.