So I'm going to start compiling a list of everything that needs to be done in order to do an ATX to MTX swap. I'm also going to post the pictures that I have taken during this process to post up on the wiki. I wanted to include this in the forums as well so that people can search for this info and see it.
As I go with this I would like people to ask for clarification on spots that I am unclear on. Also, if you have anything to add to this information I would like you to add that as well. This will probably be a slow process as I am still doing the swap.
First thing I'll list will be parts needed. Followed by what needs to go where. Finally any problems that I encountered along the way.
I don't have pictures of every single thing that needs to be done. This is not something that I want to spoon feed to people. I'm going to make the assumption that whoever is attempting this swap is fairly proficient with a wrench. I'm also assuming that you will be able to figure out how to get the engine/transmission out of your car.
About the only two things that I will suggest for pulling the motor/transmission is that you invest in some duct tape and a sharpie marker. It's amazing how easy it is to forget what goes where on the wiring harness when the car is sitting on jacks for a week or two. Or in my case about 5-6 weeks. The other is putting any and all loose bolts nuts back as soon as possible. When you pull the side motor mount, screw the nuts and bolts back into their respective mounting points as soon as you pull the half of the mount out. Again this will save you much headache later on.
I'll probably start uploading and cropping pictures at some point tomorrow. It's late now and I need sleep. Sorry for rambling.