I decided to clean up all the dodgy wiring, in my 88 model GQ patrol LWB petrol carby, that i did under the dashboard from a while back. Fix all the stuff ups, put some relays and fuses in

ANYWAY...what looks to be the alarm box (is connected to wires from the ignition, and most of it is black wiring) had two plugs in the back of it. They look a bit like computer plugs (like the one you used to plug the CD drive directly into the sound card kinda plugs). I decided to disconnect them while i was cleaning it all up so stuff was easier to get to.
Now the problem is when i was putting everything back together, i cant find one of the plugs. It couldn't have gone far, but I still cant find it. Anyway i plugged the one i found back in. So there is still one missing. Now what happens is when i start the car, it starts and runs but differently. Like it rev's higher (about 1200rpm) and it has sort of a clunking sound (yeah i know, not good). But before i played around with the wires it ran normally. Now i know probably the only fix is to plug that wire in but now im curious to how that plug has affected the way the engine runs differently. I thought the alarm wires would either make the car run, or not at all - rather than running but weirdly (if that makes sense).
Has anyone come across this problem before?
Cheers
Pete