bell housing wont bolt to block flush

i have a 91, 331 and a 71 c4 i am combining. it was a 5 speed before now going to an automatic. when i bolt down the bell housing it always leave a small gap on one either left or right side. don't know what to do. the converter seated right, and lined up with flex plate fine.
also it was a manual before as i said i did not take out the throw out bearing is that the problem. if it is what do i replace it with? its almost like it is wabeling form left to right when i tighten down one side. like something in the middle is putting pressure on it.

Did you remove the pilot bearing in the end of the crankshaft? You wouldn't use that for an automatic.

Did you remember to put the block plate on before the flywheel/flexplate? If not that would leave a small gap between the bellhousing and block. 

I agree with pilot bearing still in there or TC not seated properly. Please tell us that you did NOT try to bolt it down even though it had the gap? If you did you may have ruined the front pump on the trans. It is easy to hurt the front pump forcing the trans to mate with the motor. Also if this is an aftermarket TC make sure the pilot is not too long. I ordered a Revmax TC and I ended up grinding the pilot snout down to take up a gap between the TC and flexplate (flywheel). This also caused other issues and ended up taking out my thrust bearing in the motor and also my front pump in the trans! Be careful with the step you are on as alot of things can easily go wrong.

its is the pilot bearing i have searched around that is the only issue it could be im pretty sure. and  how would you check if you ruined the front pump on the trans because i dint force it but had to find out that it dint go on together some how...... 

I THINK the transmission should be OK. It sounds like the convertor is seated properly in the transmission but being held back by the pilot bearing which in turn is keeping the engine and trans from coming together completely. Joe's method of bearing removal is the only way I've heard of. I've tried it and it works.