I had the same problem when I was taking the engine out of a Mercury Sable. It turns out that a bolt on the starter was holding them together. I know that a Sable is no VR-4, but you might want to check.
Remove the motor with the trans attached. It comes out really easy that way. The trans is bolted to the block with several long bolts and then you have to be able to pull the motor away from the trans far enough to clear the input shaft. Much easier just to take out both and take it apart once the motor is on the ground. Edit- oops I guess you did that and now you're just trying to pull them apart. It shoud just be a few bolts. Mine just slid off once I removed the bolts.
This is the shaft that comes OUT of the trans, and plugs INTO the clutch assembly. It's long, about 4 inches if I remember correctly. About 1.5 inches goes INTO the clutch. So you have to create a gap about that wide.
It's been a month of so since we swapped my trans, so I don't remember exactly, but if you've removed the starter, and all the necessary bolts, then the only thing that would prevent the engine from going up, is that shaft.
thanks everyone... unfortunatley I got it off before seeing the suggestions.. I just put my feet on the engine mounts and pulled it of using my legs... came right off.. of course I had it in my lap then
1. The bolts on the top of the transmission into the engine.
2. There transmission stays bolt to the engine and transmission.
3. There are 2 bolts through the engine mount brackets that bolt into the transmission. They are above the transmsions stays.
The other problem you might be having is the throughout bearing snaps onto the clutch pivot arm. I had to pry my transmission off gently. And then not so gently The transmission come off with a loud pop! I though I had broken something, maybe I did ? but I replaced the throughout bearing when I replaced the clutch so there was no problems.
When I installed the engine I installed it with the transmission attached. I would suggest trying that.
I just noticed you got the trans out. already, congradulations.
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