Windshield Wipers Won't Turn On

I picked up a 99 roush mustang gt about a year ago. The car has been sitting in my garage since and I am getting ready to put in back on the road.

The previous owner has done a lot of work to the car which include a vortech S trim supercharger with 10rib pulley system and a monster intercooler, stage 3 cams and a P51 intake manifold with a various of other parts too...(lots to list)

But here's my issue...the wipers worked when I bought the car. I began to fix all the mess of bad wiring the previous owner left me. Under the dash there was thousands of cables running in all directions. With great care I followed each cable and either removed it, shorted it or carefully loomed it to look factory. Majority of the cables where from a high end stereo system that the previous owner removed but left all the cables behind. There was also a lot of wires that ran to gauges, switches and misc of stuff that were no longer there. So basically I removed anything that wasn't connected to something and whatever was still connected I just cleaned it up by putting it all into a loom and zip tie it into place. After fixing all the cables, the wipers stopped working.

After many google searches, here's what I have done so far.
I checked all the fuses (all look good).
I check the relay (I even replaced it with a relay that was right next to it and nothing).
I check for voltage at the relay (good) but no voltage to the motor.

I saw a article about a module under the dash that also controls the wiper system. But I wasn't able to located it. I did see a black box just over the fuse panel with a lot of wires coming out of it. But nothing else. What is that black box over the fuse box???

ANY HELP WOULD BE VERY MUCH APPRECIATED.


Off topic question..
There is another module (metal box with lot of wires coming out of it) in the passenger side fender. What is that for??
There is also another box (small black box with one big fuse in it) on the passenger side (where the filter box would be located). What is that for??
 
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Off topic question..
There is another module (metal box with lot of wires coming out of it) in the passenger side fender. What is that for??
There is also another box (small black box with one big fuse in it) on the passenger side (where the filter box would be located). What is that for??
The box in the front right side fender well is the CCRM. It's a relay box for the PCM, fuel pump, AC clutch, and cooling fan.

The small black box with one big "circuit breaker" is the CB for the low speed cooling fan.

After many google searches, here's what I have done so far.
I checked all the fuses (all look good).
I check the relay (I even replaced it with a relay that was right next to it and nothing).
I check for voltage at the relay (good) but no voltage to the motor.

I saw a article about a module under the dash that also controls the wiper system. But I wasn't able to located it. I did see a black box just over the fuse panel with a lot of wires coming out of it. But nothing else. What is that black box over the fuse box???
The wiper systems are some of the more difficult to trouble shoot. There are several places where they "could" break down (and you have not checked all of them).

Examples:
  • There are TWO wiper relays. Low speed and high speed.
  • there is the GEM unit that handles delay
  • the is the control handle that is part of the multi-function switch
  • there are the wiper motors them selves
  • there are the park position switches inside the wiper assembly
  • there are TWO grounds associated with the wipers. One in the engine bay the other behind the center console.
This is a case where having a full set of wiring diagrams almost becomes a necessity. If interested in getting a set for yourself I maybe able to help. PM if interested.

If looking for an educated guess, check all of the black wires and black wires with a white stripe for low resistance all the way back to battery negative. Make sure there is no current flow as this will make any resistance reading incorrect. Perhaps pull the battery positive. Pay special attention to the GEM and the wiper motor connector.
 
Since they worked before you cleaned up the wiring I would get a schematic and see which wiper wires might be affected by your clean up. First thing I do when getting another car is to pick up the FACTORY Shop Manual it is worth its weight in gold and if you sell the car you can sell the Manual and get your money back. Makes for very interesting reading too. Check the fuses using an ohmeter or continuity checker, I have seen bad ones that looked OK to the naked(and tired/thrashed) eye.