I am going to start from the beginning.
Info first,

I have a 2003 F350 Super Duty 6.0L Crew Cab Lariat 4x4 signal rear wheels Ford tow package. After market options Bully dog power put and outlook controller.

Next the problems When they started and order pleas stay with me.

I purchased a goose neck horse trailer and after hooking it up, plugin in the tight and break round plug I found that the trailer lights did not work. I inspected the plug on my truck I found that the wires were cut next to the plug so I purchased a after market plug and swapped the two out and the lights worked. Excepted the right turn signal did not work.

I thought I was good and then the problems started during the six hour trip home at night my turn lights and break lights ceased to work on my truck and trailer the running lights and head lights work on both. After I returned home I looked for shorts and bad fuses I never found any.

After that I started to accumulate problems.

The Outlook controller would occasionally loose signal and turn off and on and the door ajar is on all the time. After that the I had the oil filter fail and pieces of it went through the IPR screen causing the IPR to fail I know its unrelated but it is. After having a no start condition and replacing the IPR all my gauges would go peg to peg when trying to start. I put a long hard charge on the batteries and got them to a full charge of 12.6CV and had no problem starting any more. I did find at the time I hooked up the charger is that one of the batteries blew off one of the cell covers.

But what happened next.

The truck lost full electrical systems as in the 4x4 switch quit working, the power locks quit working, door chimes quit, the transmission would not shift into overdrive and the tow light flash and now the Outlook Controller flashes on and off so bad I can hardly get the codes off it. The auto headlight quit.

Most of the things I could reset by un plugging fuses and relays to get them to work.

OK the now, I changed the batteries today with new ones and found out the old ones were only at 75% and that fixed some of the problems.
The problems I still have is the transmission, turn signals, break lights and Outlook flashing on and off. By the way the Outlook is plugged in the systems plug under the dash.
These are my codes
P0360 ignition coil j primary (I do not know what this is or where I can find it.)
P0401 Exhaust Gas Recirculation Flow Insufficient (Is this the EGR cooler I did a EGR Delete by puting freeze plugs in both ends)
P0603 Powertrain Control Module Keep Alive Memory (KAM) Error ( I have no clue about this, this started when I lost the IPR durring all that cranking.)

 

The P0603 if from the the tuner and nothing to worry about, the rest sounds like a ground problem. Was thinking Ign Sw contact but brake lts are hot bat bus, so thats not it,

 

I drove the truck and payed attention more to how the transmission was shifting and once it up shifts it does not want to down shift. it seams to stay in 4th even after stopping. to reset I need to stop put it in park and turn off the truck to reset the problem. Then the problem starts all over. I still think it's electrical.

 

were these problems there before the trailer plug?
P0401 is EGR delete without turning the sensor off, need a tuner to do that, $400
P0603, battery disconnected did that.
P0360... never heard of that.

 

The Bully Dog has a bad rep. for destroying TS trannys.

 

No the problems that was the start point. The problems accelerated when the IPR failed and Then the batteries failed.

 

I here that often but I never met any one that has had that happen to them. Or talked to any one that knows any one that has had the problem. So far I believe my problems are electrical. Because the transmission is only one part of the problem. Why would my OBD connector fail?

 

The OBD2 port on Fords do not like Bully Dog Tuners.....

Just kidding.

You might remove the cover for the CJB located under the steering wheel and check the connections supplying it.
Voltage that supplies the OBD2 is fed from a fuse in the CJB and it is shared with the cigar lighter.

 

I ended up taking my truck to the ford dealer and found that the the GCM fried when one of the Batteries shorted. The ford mechanic also told me that he doesn't see problems with the Bully Dog. The ford dealer is charging me $179.00 Install and programming. Now That's a deal!

 

That is a deal, I am surprised just the labor was not $100. Those are a PITA to get at if you don't know what to look/feel for.

 

Asheville NC Ford took good care of me.