yeah.. I know. Ive read a bunch that are similar to my problem.. but here goes.
I own a 1999 F150 Ext Cab 4.2L V-8 2wheel drive, automatic. Im the only owner. with over 143k miles on original tranny.. This truck is my baby.

In 2007 we had problems with it not having any pick up and go. after changing damn near half the exhaust and intake and the PCM, we discovered the transmission needed to be flushed. problem was fixed. Truck ran great, until we needed to use the spare key... to our surprise we discovered the key had never been reprogrammed to the new PCM. Suddenly the truck would throw the anti theft, and refuse to start. After 30 minutes of trying the key, waiting 30 seconds after the light flashed.. it would finally restart.. only to die on us while driving down the highway. This got old fast.

Dealership checked everything, reprogrammed the keys, swore it was fixed and sent us on our way. That worked for about 3 days.. Then it started again. No rhyme or reason. It would just decide not to start. When I say not start, I do mean, that the engine does turn, the fuel pump does engage. everything does what its supposed to. But it wont turn over. We've replaced the DPFE sensor, the EGR valve, spark plugs, the coils, checked fuses, wiring, hoses, fuel pump replaced, fuel filter replaced, reset the PCM multiple times, changed out the front windshield because the dealership swore that was the problem, getting moisture into the GEM. The O2 Sensor is new, and the idling sensor is still good. After being at the dealership for days, they tell me everything is running like it should be and they dont understand what my complaint is.

It may run for a day, purring like a dream. The next day, start it, it suddenly dies, and throws the anti theft system into a blinking frenzy. Then refuses to start at all. Some days it wont let you start it at all, just put the key in, start to turn it, and the theft light begins blinking. If you continue to turn the key, engine cranks, but wont turn over.

the Ford Dealership is at a loss. Pretty much all they tell me is to trade it in. A few other mechanics have said its either a bad PCM or a bad GEM. I need to know is there a way to test the two to figure out which is bad. Ive read that the PCM will not let the truck run if something is wrong.. but what? the keys are working. The system reads the keys. it has to, as it will start, but not always.

The PCM was put in by the dealership in 2007 brand new. Ive spent a small fortune trying to solve this, and am at my ropes end. Im so disgusted with seeing it sitting in my drive, but trading it in is not an option right now. The battery is new and fitted by Interstate.

It has thrown codes before, the SES light used to come on throwing the craziest codes that all the technicians were left scratching their heads swearing the truck was possessed. The last mechanic I spoke to recently was for Chevy and said the problem lies with the GEM getting moisture in it and shorting out. When we replaced the windshield, we discovered the PCM had been getting moisture in it as well. I've never driven thru high water with the truck, but it does get moist down here as we are in South Texas.

Any help is appreciated. Is there something we are overlooking? Anyone else stuck where I am? Please Help!

 

It sounds like the pcm to me, Have you ever asked them to reflsh the pcm? There may be a short around the pcm it self making it do strange things. Maybe take it to another ford dealer and see what they say. Just seem like it has something to do with the pcm. Goodluck

 

I am suprised at the lack of good technical support expertise in your discription of the events.
I get from your total discription that the PATS system has an intermittant condition.
If so, the motor will not start by design because the PATS has to communicate with the PCM as a means of theft protection so a fault will cause the same no start condition.
In the PCM, there is a software block called the VID where a bit must be present to satify the start chain as well as other ID info about the truck's build.
Normally if a fault with this system occurs there is a code to tell that fact.
Is this code what the mechanics did not know about?
Do you know, what was the code/s are?
As well, the 30 minute delay to PATS reset is a normal chain of events.
If there is a failure in the PATS system, turn on the ignition to RUN and let it at that for more than a minuite. If there is a PATS fault, the theift lamp will flash telling you there is an issue.
Also if the dash is electronic it has it's own diagnostics that can be code read from the mileage display. It will often supply an indication that backs up the same fault seen by the PCM, just that it is on the other end of the communications bus between the PATS system from the PCM.
The PATS and the PCM must be programmed at the same time with two keys. They cannot be seperated on a service basis.
Hope this is a help to you but some one has to understand this and take a look at the possibility.
May be helpfull to print this reply and show it to dealer svc (if) they don't know what to look for.
Good luck.

 

Thank you so much for the replies!!
The techs down here really arent too bright. The codes were too numerous to recall each one. It went from EGR malfunction, to Low Voltage. Recently we replaced the battery with a new interstate one, and was surprised to find out the current battery was the wrong size for the truck. Interstate upgraded the battery and the Low Voltage code stopped being an issue.
The Dash is electronic, and in the mileage box, it will show all dashes when it refuses to start. Tried the key thing, and it blinks normally once the minute has gone by, but the mileage still shows dashes.
My brother decided to spend some time problem solving this thing. He pulled the PCM and discovered the entire top of it was corroded. We opened it up, and the board is covered in rust and water stains. The floor board under the computer was soaked. When looking at where the PCM sits, we discovered the lip of the drain fin on the hood was no longer tacked down completely. we duct taped the hole where the PCM goes, poured water on the windshield and watched as the water pooled up and started running under the drain fin, trickling down right on the connector for the PCM. the weak rubber seal they have isnt enough to prevent the water from getting into the actual system.
Also discovered the ford dealership that put in my "new" PCM in 2007 ripped me off. The PCM was used and spray painted gold.
When the truck runs and shuts itself down, the PATS kicks in and refuses to let the truck start. Could the PCM be shorting out? Sending erroneous codes to the PATS system?
When you mention both keys must be present when programed.. they werent. the dealership only had the one key and told us the other would program when we started the truck with it. It took them half a day to get it programed to start.
Since it has to be programed by a dealership, we are talking with the head mechanic at the Chevy place in town. They are looking for a new computer for the truck (apparently they have to match the PCM up?) and will be installing and programming it. Then we get the fun of waterproofing the PCM.