Agreed, clean up what you have. I was in a similar position with my YJ. Stock 258 but the wiring was a mess. The only wires you should need on that harness are the distro/ignition wires that are horizontal on the firewall, the vertical wires on the drivers side and the headlight wiring the gos down the drivers side fender. Google the stock 87 wiring harness, start with the wires that dont go to anything and delete them making sure first that your not going to need them. The wiring on my YJ was too thin of gauge for the ignition and the fool used duct tape to wrap his connections so source out anything like that and correct it. If your fooling with wiring its not a bad time to consider ground upgrades.
This is everything I pulled out of my wrangler: