lining up transmission on 98 sonoma

I just got a new engine, 2.2 for my 98 , it was out of a 99 sonoma I had to change out the intake and a few other things, but my proble is lining up the transmission to the engine. The transmission is 5 speed and it seems to me that the though -out bearing is hitting the pressureplate, the book says it will just slide on, but I am not having any luck. Do I need to release the clutch? please someone help. if you want to post do so, or email me [email protected] thanks Joe any help is more than welcome..