ok so i just made it back from the J/Y and i gotta good look at a factory 5spd dohc harness and also took a good look at my sohc auto harness in my car. this is what i found. (sorry bout the huge photos i hoped it would help you see things)
Photo of brake pedal sensors and relay -- 90 auto w/cruise(the relay is above and to the right of the sensors perched atop the brake pedal assembly - you can see the botom of the bracket that holds it in)
Photo of door subharness driver -- 93 manual w/cruise(top left blue and white connector only)
Photo of radio and climate control area -- 93 manual w/cruise
from these pictures i would have to say that your old harness is a 89 - 90 auto w/cruise and your new one is a 91 - 94 manual. your strange plug likely goes to the back of the clutch pedal and needs connected or bridged to start the car. the two connectors do go to the radio the smaller one goes to the optional tape deck. as far as where your doors hook up either your not looking hard enuff or your dohc car came with no radio (either is possible i really dont know i will look again at my other dohc harness later as its not here) there are a few more photos on my photobucket page
http://photobucket.com/michaelschwartz and i will post more later. as far as cutting and soldering i would hook everything you know up first, the only thing i see you may need to do is check on that clutch plug(?) and as far as my doors i would simply run new speaker wires.