Scott; I had a mess like that for a long time. I finally had to have the wiring harness replaced, and used the Ron Francis kit (www.ronfranciswiring.com), and the man that did the job ran everything behind the fenders and hid most of the wiring. Here are a couple pics underhood. Hope it helps you. See if you can do something similar.
Start over. Now you know what wires you need for what. Get a little relay box and make your own harness. Its just time to make the harness and route it neatly with convolute tubing (BLACK). Crimp connectors look awful and shouldnt be visible if possible. Thats were the relay box comes in. If you must use crimp conn. get the ones with heat shrink attached. They look much neater and more professional. I've made lots of harnesses for newer vehicles. Its kind of fun. I'm doing a relay box for mine this week along with the electric fan. I'll post pics when its done. Got the fan fitted today. Jeep Liberty fan(19"0 with shroud). Perfect fit with some mods to the shroud.
I used a relay rack from a late 80's Caravan. There's a 3-relay rack also under the Caravan's hood also.
first off you dont need to have any of that suff in that location. sence your bat is in the trunk you can relocate all that stuff to different locations. on my car the starter solinoid is on the inside of the fire wall right under the heater box. my msd is inside my custom dash. before i had it siting on the tray under the dash with the intent of mounting it on the back side of the tray. on Mo's car we put the starter solinoid in the trunk near the batery. his msd is also in his trunk. when we swaped his starter out with a newer style that has the solinoid on top of it we took the solinoid out of the trunk and just put relay on the inside of the fire wall under the heater box to trigger the starter.
