Hiding Wires
Time to take your engine bay to the next level of clean...

"The Rules"
1. There's really no way to mess this up. Don't worry. The only thing that can be put together incorrectly is the coil. Take pictures, draw diagrams, whatever works.
2. All you need to know is the basic idea, there is no one way to do this. All cars will
differ, and so will your mounting points, etc.
3. If it doesn't make sense in this tutorial, it will once you dig into your wires.
4. This can take anywhere from 1-3 hours per side.
5. Use wiper tubing to line the holes (coil wire, etc.) for cleanliness and safety.

So with that out of the way, let's begin!

Jack up the car, remove the front wheels and fendewells. The fenderwells are just held in by a few Phillips-head screws. Give it a little elbow grease and it will come loose. Snake it out of place and you are ready to begin. I also suggest a dust mask when doing this step!
Remove the wire looms & electrical tape from the wiring harnesses in the engine bay so you can begin. Some harnesses are made up of smaller harnesses, and in such cases it is a good idea to unravel them from each other so you know what's what.

The Firewall
We might as well start with the easy one first, right?
You can gut your interior and run the main harness behind the dash, and more power to you if this is your chosen path. I have no help to offer in this case except my best wishes to you.

To make it a simpler task, all you need to do is cut the mounting pegs that hold the wire harness to the firewall, and tuck the harness below the "pinch weld" holding the firewall together. For the brake lines, they are handled in the same manner. Likewise you can bend up custom brakelines and reroute them all over the place to keep them out of view.
The Vacuum Tree
This will require lengthening a couple hoses; the brake booster and cruise control lines. Depending on factory tolerances you may need to lengthen more. I dismounted the tree from its stock location and put it into the fender in the area where the fender meets the body, although it can be mounted anywhere there is room. Disconnect hoses, mount the tree in its new location, and reconnect them. Lengthen those which need it, and make sure to avoid kinking any hoses.
The Strut Towers
To put the harnesses into their new home, you need to:
1. Disconnect the plugs
2. Put the rearmost half of the harness through the back of the strut tower hole into the fenderwell.
3. Put the foremost half of the harness through the open area near the headlights and into the fenderwell.
4. Connect them inside the fenderwell.
5. Tape or loom (or both) the harnesses and ziptie them in place.

You'll most likely have to enlarge the holes in the back of the strut tower to fit the harnesses through, unless you choose to cut the wires in half and solder them back together.

The Starter Solenoid
Remove all wires and breaker from the solenoid. Be sure to mark the order in which they came off (photo, diagram, etc.) Simply unbolt the solenoid and put it in its new location (directly under the framerail where the fender bolts to was my choice and allowed me to forego any wire-lenghtening other than battery cables).

The wires are entered into the fenderwell in the same manner as the others. Depending how clean you want this to be, the battery cables will need to be replaced some which are longer. I opted to route all wires from the battery TO the open headlight area TO the fenderwell TO the solenoid. The starter cable went from the headlight area UNDER the framerail across to the passenger side and down to the starter. There are easier ways, but it all depends on how clean you want this to be.

Relays ('92-'93 Mustangs)
1992-93 Mustangs have the AC & fuel pump relays mounted right on the passenger side strut tower. These can be put into the fenderwell and mounted along with the harnesses.