Time For a rebuild

ok did some more work today, decided it was a good time to mock the engine in the car and try the trans to it. engine went in without a hitch, slid the trans under the car and then with the floor jack started to put the trans in place. got it up and in but the engine and trans will not sit flush together. tried everything and the drivers side is 1/4 inch space and the passenger side touches. The dowels are in the holes and the bolt holes line up but no go. I will post some picks later. Has anyone had this problem? Next step is to pull it all out and try it on the ground and see if that helps.

Trevor