it will work fine with a 4 speed. The way I wire it, the computer has no control over, and needs no inputs form, the transmission EXCEPT the neutral safety switch. All the neutral safety switch does is grounds the circuit when in N or Park, and allows the starter relay to then become active. If running a 4 speed, all you have to do is take the center wire from the neural safety switch plug and either ground it permanently ( the computer thinks it is always in park/neutral) OR do it the right way and run that wire up to the clutch pedal safety switch, so the car will only start when the clutch pedal is depressed, just like factory.
the only other wiring going to the transmission is the VSS (vehicle speed sensor), but that is not necessary to use, you can leave it unplugged. It is only required if 1), you are running an electronic speedometer, or 2), you want to at some point wire cruise control back into the harness. Other than that, leave it unplugged and run your original cable driven speedometer instead.
you don't need a manual trans specific computer, any dakota/ram/van 92-95 computer will work fine. They all use different color wiring in the harness, but the PCM pinout is the same.
any more questions, feel free to ask!
Doug
