Is the pressure plate in the right way?
Slide the motor in as far as you can get it to the transmission, than bolt 4 extra long bolts and adjust the bolts so that all four corners are square. You should be able to giggle either the motor or the transmission and it should slide right together.
If it doesn't, try turning each bolt a little at a time and see if it will slide together that way. Do NOT use excessive force. If you can't get it together that way. I suggest your pilot bushing is too tight and needs to be reamed out.[It happens all the time} or something else is wrong and it will need to come apart.