I had a bunch of trouble with mine at first. But mine is a McLeod dual disc RST version, and not much room to put the trans in an A body. Anyways, I used the plastic alignment tool and thought all was well. I was very careful to get it nice and centered, as best I could tell.

Couldn't get the trans in at all....same thing as you have noticed.

I ended up putting a spare input shaft that my dad had, in there. Result,...not lined up good enough. You could tell that because the actual direct gear on that input shaft was off center to the bellhousing center.

Used the input shaft to re align the clutch and it worked perfect.