Help! DTC P0340 Ford can't resolve problem

To make a long story short, one month ago I was driving to work and hit a puddle eh Lake of water, a few hours later I got a Check Engine Light, SCT showed DTC P0340 Cam Positon Sensor (A) error.
Mods: were Steeda Underdrive Pulleys (UDP), K&N CAI, Steel braided hose covers and Magna Clamps, Plenum Cover, Pioneer Avic-D1 (this is important later in the story). I flashed the PCM back to Stock, reinstalled the Stock Air Box and took the car to Dealer#1, after several days of fighting about the UDP and invoking the Magnason Moss Act and the FOMOCO denying Warranty, they finally fix the alternator because of a TSB showing this exact issue being caused by a faulty Diode in the generator.

I get home after a few days in a performance shop getting 4.10 gears and a the DTC P0340 showed up again, I removed the UDP's and put car tune back to stock once again, still that error (BTW there was performance issues associated with this code, the throttle was boggy at low speeds)

I take the car to a second Dealer (well call him #2) since Dealer#1 gave me a hard time about aftermarket parts, after a week the dealer calls back and says they have tried everything, they replaced the PCM and the Cam Position sensors and still are getting the DTC P0340.

So dealer#2 is not denying warranty because of aftermarket parts, they are saying that They can't figure out what the problem is, so to eliminate all potential problems, FOMOCO is asking that I remove ALL Aftermarket parts so that they can continue to repair my car. they use diagnostic step sheets to try to figure out service issues, the dealer is telling me that they have tried ALL diagnostic procedures thus far, so they are now pointing to the aftermarket parts, None of which are Engine performance parts.

Steel Braided Hose / line covers and Magna Clamps (Possable RF interferance)
Pioneer AVIC-D1 Nav System (Possable RF interferance)
Midwest Plenum Cover (Possable RF interferance)
Sequental Taillights (Possable RF interferance)
FFRP 4.10 Gears (Possable causing PCM failure)
Polished Stock Aluminum Valve Covers (Possable RF interferance) Never removed
Non Ford MOCO Approved Air in the Tires, (Possable vibration)
Non Ford MOCO Approved Wax/Polish (Possable wind turbulance)

After Above list is taken care of, then the Dealer can continue to diagnose the problem

Has anyone seen this issue? any ideas? I hate to strip the car down, Help please....

I have posted this story on other forums with the same response,

I pulled everything from the car, including the Pioneer Radio (Nav) and still getting the code, I think the service advisor was shocked to see me, he thought if I took that stuff off the car would work again. He was wrong, Still getting P0340 and P0344. I did not change the gears out since that would cost some money.

Any Ideas, Anyone ???

I Just told the Service Advisor this, I asked him to test it again, make sure that the first dealer actually replaced the alternator. They were going to run the tests outlined in the TSB 06-2-3 in the AM...
Thanks..

Ok, Dealer is pulling the Valve covers today,

Just to show that I an not loking about removing the braided hose covers...
Here is the proof, Oh an the Gears causing problems with engine