Part of the reason why I decided to rewire the ECU: (not very tidy)
To tuck everything in the engine bay, I decided to put all relay and fuse boxes into the rear bin. To start, I took out the front body harness (the one that wraps from the driver side foot well, around the front of the car, and into the passenger side foot well).
Identify the plugs you don't need in the engine bay and snip the wires, then snip the same wire at it's other end to delete the wire completely. For example, I'm deleting the fan relays and using my ecu to control the fans, so I snipped every wire at the relay, then I went and snipped the other end of the wires at the relay and fuse boxes and another other plugs they went to.
Label each wire that you are keeping but relocating (all wires going to the relay box got an "R", all wires going to the Fuse box got an "F". There are other wires that go to the large Grey connectors next to the fuse box, I gave these all numbers.
The last few wires left just run from the driver side foot well to the passenger side foot well. I labeled these all with a number as well. After snipping these off, I ended up with a driver side harness and a passenger side harness. There are barely any wires left on the passenger side. and the ones that connect to the driver will now be connected inside the car, instead of wrapping all the way around the front end.
Stripped harness, being labeled and cut:
Everything cut except for the 6 remaining wires that just run from foot well to foot well:
You can see the bulk of the wires end up on the driver side:
Once it's in two pieces, put it back in the car and connect the remaining connectors to the fuse box by the clutch pedal and all of the other connectors down there. Once you know where all the connectors go, tape it all off so that the it all fits nicely and each wire goes where it's needed. Then remove and completely wrap it.
Driver side, wrapped up. Now the wires that run to the rear of the car for the relay and fuse boxes need to be extended and wrapped.
This is the hardest part, now I just need to run the new wires for the ECU and alarm system.