Someone please help me. I have my CA18DET in my 93 Hatch. The only problem arising at the moment is that the transmission refuses to want to line up with the driveshaft properly and will, therefore, not let the crossmember line up with the holes to mount it

Is there something I am missing. I had the rear of the car on jackstands to be able to rotate the driveshaft but it just says no. It's really pissing me off now. The engine has been mounted since Monday and I got the time today to mount the trans etc. Someone tell me what I'm missing or doing wrong.
Thanks!~Ian