Get a 00 SE throttle cable, much shorter.
The only way to a tuck right is to redo everything.
Quick list:
1. Label all connections while removing the harness
2. Strip the harness down to the wires and tape with masking tap every foot or so and junction.
3. Pull any un-needed wires, cruise, wipers, AC, PS, ect.
4. Put the harness back in the car and figure out how you want the wires routed. (I prefer running wires on each side depending on where they go)
5. Move all relays and fuse boxes inside the cabin, behind the glove box is a good location.
6. Extend/shorten the wires as needed to get them where they need to go.
7. Tape the whole harness then loom and add tape every so often to hold the loom and at junctions.
You will end up with a lot less wire in the bay so they are easier to hide. There are a lot of wires that go from the relay box to fuse box that run from one side to the other, relocating the fuses and relays next to each other uses less wire.
This process is not easy or quick but you wont have any issues as long as you solder and heat shrink everything. Stagger any solder joints so a bulge is not created.
5.