im not sure what plug exactly but i would figure.. its a open bridge between the plugs so that means it should be telling hte computer dont.. but then again it had to start unless its hooked to some other thing for the aod..
did you do a t-5 swap? assuming so, then you can just leave the one on the pedal on there. It is just a loop to bypass the NSS. But just remember that the car will start without the pedal being in. If you want the NSS, then in the wiring loom under the dash there is an extra plug near the top of the pedals that will fit on there for that.
as for the tranny-
I didn't buy any extra wires or anything when I whole v-8 conversion for the tranny. I just hooked up what I could and let it be. I am not sure what all the terminals do on the tranny but the ones I hooked up worked for the reverse lights and I know I left something unplugged (because I didn't have anything for it.) Someone else on here can tell you what exactly everything is for.