When I put the T18a in my CJ-5, I had the same trouble. Pulled it out several times. Even got out the calipers and measured the pilot bushing and input shaft. Cussed it. cussed some more, pulled it out, measured again, stared at it a while, and on and on. Checked and rechecked with the alignment tool. Measured the alignment tool against the input shaft. This went on for a couple of hours of fighting it.
Decided to try it one more time. Slipped right in on the first try. Nothing had changed. Go figure.
Sorry this doesn't help much. But just check and recheck everything.
