I believe there may be confusion on what and how you want to do.

There are 3 schools of thought on removing the engine.

1. Remove the engine & transmission a the same time.
2. Remove the engine & leave the transmission in the car.
3. Remove the transmission and then remove the engine.

I believe you are going for option 2, correct me if I am wrong.

For an Automatics when you unbolt the engine from the torque convertor. You will only have to separate the engine from the transmission about an inch or two to be fully separated. Then you could lift the engine straight up with no binding between the two.

For a manual transmission it is common to leave the clutch assembled to the engine, so a manual transmission input shaft has to be pulled out of the clutch to be free and clear. This takes about 4 to 8 inches of separation.

I think you what you are wanting to do is unbolt the pressure plate from the flywheel like you would unbolt the torque convertor from the flexplate. Am I correct?

If you unbolt the pressure plate from the flywheel it will make it a shorter distance to separate the two, but you will have parts flopping around inside the bell housing and falling out when they are fully separated. It is clunky and not the best option.

I have left the transmission in place and forced the engine and transmission apart and it did okay but a less dramatic way and better way would be to pull the transmission, or at least pull it back a good bit and then remove the engine. This means removing the shifter or at least the handle in some cases.

The most common danger in forcing them apart is that you would damage the sleeve that the throw-out bearing rides on sticking out of the Input Shaft bearing retainer.

I suggest option 1 or 3 if you are new to pulling them. Option 2 is ok if you have the room but big engines in small cars usually don't.

I have had terribly bad luck with getting the clutch to align even with the tool or even spare input shafts. I usually leave the bolts on the pressure plate loose enough to slide the disk inside the clutch but tight enough to hold it in place if you don't force it to slide. Once it is together I bolt the pressure plate down. Not an option on most racing bell-housings though.

Hope it helps.