Okay now here's an update...

It's gotten worse. Now the truck won't even turn over.

I took out the fuse box / GEM module, set it in rice over night and put dielectric grease on all the terminals before putting it back in truck. When I hooked battery up there was a clicking coming from the ABS pump or whatever you call that thing on driver side with all brake lines going to it. Then when I tried to start it the ACC Delay Relay and possibly the One Touch Down Window Relay were clicking in fuse box with no turn over.

Put a new battery and new starter solenoid.... No Change. Jumped the truck from the solenoid and started right up and ran fine.

With the truck off I shifted from Park to Reverse and all interior lights went off and 4x4 light popped up. Went to Neutral and went back to normal. Still clicking when tried to start, though I know it shouldn't start in anything besides Park anyways...

What in the hell is going on with this thing? Is there some fuse / relay I'm missing here or is my wiring all shot to hell? Anyone with any ideas would be greatly appreciated.

 

It doesn't sound like a PCM but might be. It also doesn't sound like you tested the GEM for moisture or looked at the ting for water intrusion evidence or you would have posted such. You test for moisture by forcing a little compressed air into the voids. If there's moisture settling inside it will be forced out another void/gap therefore confirming a moisture problem. So you could still have a GEM problem since it sounds as though you just threw the thing in a bowl of Uncle Bens and called it good.
I guess at this point, -I would definitely go through all the grounds. Since you didn't feel the to post your model year and engine I can't be specific. Fortunately they are easy to locate on this truck, -

All grounds on the firewall, there's 3
Grounds under the kick panels 2 on the drivers 1 on the passenger
Make sure to check the cab to engine ground (furthest ground to the left on the FW)
The cab to frame ground under the passenger side floorboard.
Battery to frame rail (behind the passenger side tire on the frame)
Battery to starter and engine ground to the left of the starter.

Not sure you do all that, doesn't really sound like you seriously want to fix it IMO. Regardless, there yuh go.

 

Check pcm relay. Make sure you didn't mess up any of the connectors on the back side of the fuse box.

 

All grounds are good now. Had the cab to frame on passenger side unhooked but fixed and still no change. Opened up the GEM where the motherboard is and was no water damage. Guess I'll take off again and check for moisture. It's a 2000 f150 with 5.4 and automatic trans. Thank You.

 

If your unsuccessful with finding any evidence of moisture or corrosion with the GEM, well -lets just say they usually don't get all crazy like that unless there's a reason....9 out of 10 that would be moisture. So, this might be a tough one. You may be able to narrow it down by pulling non essential fuses. If the goofiness subsides reinstall the fuses one at a time....that could pin-point a bad circuit throwing a wrench in the spokes of others. It doesn't take much to corrupt a signal or signals. Other than that, if the grounds have good contact and the GEM looks okay I would lean toward the PCM. Disconnect the battery then disconnect the PCM and PCM ground on the firewall. The PCM ground is the ground furthest to to right in the corner pass side FW across from the battery. Inspect for corrosion and water damage. These trucks leak water on that side as well. The leak through the front of the cab where at the cab over laps right in front of the windshield. Yea these trucks wouldn't make very good aquariums lol. Do all you can to confirm the problem. Guessing it's the PCM can be an expensive mistake and a hassle since this is a 2000 model. You would have to bring it to Ford in order to manipulate the PATS.

If you can get a hold of some wiring diagrams, they may help educate you with the system, I always use them when TS'ing electrical and PCM signal.

 

My truck is doing the same thing im really hoping the gem will dry out on its own.

 

Bump for an update.

The starter is turning real slow now at first and then it speeds up just enough to crank it up. Seems like this must be a ground problem? Have took off all grounds and sanded down metal bare and it still does it.

It's definitely leaking water somewhere. When I took off the side kick panel on driver side there was a puddle of water under the plastic.

Not exactly sure what to do about the starter problem. Anything I should check anywhere that would cause this all of a sudden?

 

Wet gem.

 

How did you install the light bar? Did you put holes in the truck? That windshield molding is a PITA to get to seal again. Usually the installer just puts new molding on these things.... at least here they do.

And agreed, again, this is a wet GEM issue.