To add info I didn't think about from before:
Axles - they are different. The Autos are 26spline if I'm not mistaken and the manual is a 28 spline.
Shift Linkage - just find an old P5/Protege' and grab the linkage and hardware. It installs in 10 minutes and you'll have it all done with little effort.
Clutch pedal - again, source this from your parts car. it's got a nut on top that's vertically mounted, and 2 points of contact on the firewall - one from the inside/out and the other from the outside/in (found it was best to do this with a helping hand in order to center the pushrod for the master cylinder and hold it in place while I got the inside nut tightened up first.)
Wiring: You'll have the Transmission plug in the engine bay unplugged, because there's no plug for it to connect to on the MTX. There are 2 large pins that allow you to send the start signal to the starter - for testing purposes - take some wire or something large-gauge enough to carry the current - and short them together. This (from my experience) bypasses the clutch safety switch, and the neutral safety switch. PLEASE, PLEASE, PLEASE ENSURE THE CAR IS OUT OF GEAR AND THE P.BRAKE IS SET!!!!! This is by no means a permanent solution for this, but it will allow you to test what you've done. After you've tested the conenctions and made sure the car starts - then you can cut those wires from that plug and join them together properly with solder, shrinkwrap, and secure them somewhere. There are also a few other wires there that will need to be connected (Reverse lights, NSS).
I still ran the ATX ECU on my car with the MTX. I did have a CE light, but I could at least drive it with the ATX ECU.
This is just what's coming to mind.