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It appears there are 7 bolts on the back of the transmission housing to the block. Since you are taking out the engine, you might as well take them out together. People that have just worked on their transmissions typically tip the front of the engine up with a jack, after they have disconnected the 2 motor mount retaining nuts, fuel lines, and anything else that would get in the way. You would really want to have a transmission jack to deal with the weight of it are just going to pull the transmission. It needs to be lifted up so the bolts can be removed or installed without galling the threads Harbor freight has a screw type transmission jack or you could rent one. The car needs to be up in the air enough to withdraw the transmission which would either be done on a lift or precariously on Jack stands. If your plan is to leave the transmission in the car, I haven't done that and maybe someone in the forum could comment. Seems like the motor mounts would restrict movement and it would be easier just to pull the engine and transmission together. Is it a manual or automatic?

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Thanks you for the help, and that is one beautifully clean engine! It’s an automatic, I plan to keep everything oem for the time being. I’m just hesitant to pull both due to clearance issues. Is there anything I can do to either avoid clearance issues? And would it still be possible to unbolt that in its spot?
 

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In the picture, it looks like it has knurling on it and an odd shape that makes me wonder what you are truly looking at. Are you certain it's a fastener holding the trans/engine together? I've never seen something like that - almost looks like a screw open bleeder or vent vs a fastener. It certainly doesn't look like a typical bell housing bolt which is invariably a stout hex headed bolt as it has to seriously clamp two major components together.

I'd think you'd be way ahead of the game to follow Bruder's advice. On a rear wheel drive vehicle, generally the trans can come back off the engine if the engine's front is tilted up exactly as he describes. That will give you access to the top bell housing bolts, which are always a pain. Have at least 30" of extension and a swivel available and a cheap electric impact tool will pay off big if you can't get them by hand.

Removing the engine (massive numbers of connections) to get to the tranny just to remove it on a RWD vehicle is a tough proposition. The tranny has like 15 bolts to remove it and you have to take it out anyhow, right?

Since you have the engine pretty much loose, keep going to get the motor mounts loose and see if you can tilt it to let the tranny come off easier? That's my advice, as well.
 

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I think that's just a socket over the bolt. There's four of those at the top from what I remember actually, seems like two on the top, then the rest are on or around the stiffener plates. On manual swaps people just loosen the motor mounts, then tip the rear of the engine down a bit to allow enough space to fit a >3ft long extension to get to those bolts.
 
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