2003 Suzuki Aerio Remounting Transmission

Having changed the clutch (complete clutch including pilot and thrust bearing), I am trying without success to remount the transmission to the engine. This is what I have don so far.
1) After getting the transmission in place (there is on stud that the transmission is guided into place with) I tried to manually press the transmission and engine together, but it would not budge. So I went to 2) with all the bolts that connect transmission to engine lined up correctly I tightened them up gradually one at a time so as to keep the gap at bottom and top, back and front constant. This still did not close up the gap, as it gets to the point where they will not tighten any more. Because I thought that we may not have lined the shaft up correctly, I took the transmission off to check. It seems to be lining up. But will not close. Step 3) Email someone who may recognize what I am doing wrong, or of there is a technique or trick I could use to somehow get the transmission back on. Note: I am using an engine hoist that is secured to the engine and the car is on stands in the flat garage.