I was wondering what all the differences are with the wiring harnesses between the 88 harness and the 99 harness.

I am using the 1988 wiring harness and trying to bypass buying a 99 civic si harness (for the sake of money). I already have the computer I need and the updated wires it needs to run for the sensors. The thing I keep running into is where the 88 harness places some of the wires. I have two female wires hanging on the back of the 99 motor where they were needed on the 88. The other thing I noticed that I have another open wire hanging on the right side of the 99 motor where it was used on the 88 (on the right side of the intake manifold to be exact).

Does anyone know where these might now be located? I need as many tips as possible to help me get this car running by the end of May (it's my car for school and work!).