Did your 90 have a 258?
I just got done rewiring the whole engine compartment harness of my 88, for exactly the reason you mention, with my weber and DUI I use about 1/4 of the wires in the stock harness, when I started this big project (lift, gears, engine rebuild, etc.) I decided to redo it all right.
I eliminated the emission computer, the ignition module, and the ecm. There are three harness in the engine compartment. The one that comes through the firewall in the middle (near the int/exh manifolds) is the emission computer that is located in the dash, behind the glovebox. You probably wont need any of that (ie mine is in my basement now). The other two harnesses (near the brake booster) are for the electrical system (dash sensors, main power for everything, etc.) and the headlight harness. Those two are secured with a nut, maybe 5/16 IIRC.
I gotta run now, but if you have specific questions I might be able to shed some light. I still have the 258, no V8 swap. The Chilton manual is a huge help, and its wiring diagram is 100% correct if you follow it.
Black '88YJ 4.2L
2.5" Skyjacker, 32x11.5s, 4.11s, Weber, HEI, etc.