2006 Ford F-150 Questions

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loud whinning noise when the truck is running
On and now they say the pcm is out and I need a new computer. Did they do somthing wrong when installing my battery to make my computer skrew up?
Truck's display, gauges went out and truck lost all power. Diagnostic machine said alternator. Took to a local repair shop who said wiring harness needs to be replaced ( including battery cables and a new battery). Cannot rule out alternator but "believes" alternator is good at the power source.
Driving 65 MPh truck shuts off no warning , got towed home ,now It struggles to start, when I tap on the gas it dies, If I hold gas it boggs down and smoke pour out the exhaust did have code for bank 1&2 cam senors , cam over retard ?? Now no Codes
Changed plugs and ignition coils and cleaned throttle body. Runs way better but seems to suck gas bad. Owned since new and never this poor mileage
truck ran almost perfect for 4 or5 k miles then noticed a little hesitation on the road between45 and 65 like it was not getting enough gas. also noticed the oil pump gauge not working all of the time. Started sounding like it was hot and like a diesel with valves clattering. Did,nt know if it would go dead at red lights or not but did;nt Don,t want to burn it up if it is oil pump. Want to be sure what it is before I start guessing.what parts to change.Will some synthetic oil help to keep it going for now?
I checked all fuses. Are the two of the lights on one fuse or lighting wire. Please advise ASAP
I am wanting to know how I can fix this problem

Make: Ford

Model: F-150

Engine: P1000

Year: 2006

Error codes: 4.6L

Knowledge level: I know little about cars

Help needed: Please help me find out what is going on and how to fix it.
I am an engineer and mechanic.
Have already ruled out E Brake and Fluid Level, switch and sensor good. Haynes manual (nor Google) does not show Pin #'s for the 32 pin connector to the dashboard (which i have out laying on steering column) (manual has just the wire color code), anyway .... THIS IS IMPORTANT GUYS .... it appears nothing can that Red Light on except the two items listed above, and that IS MY QUESTION !!! some ignorance on internet blogs have individuals blaming dirty fluid, thickness of pads, and hydraulic pressure, and or the propotioning valve BUT I DARE TO SAY ...... that all those things are bogus, NO NO NO, because the only circuits to turn that bulb on are the E Brake and Master Cylinder Low Level sensor ..... I just want you to please say , YES , you are right. If so, then I have a well reported on Ford flaw of leds becoming shorted "on" on their dash cluster pc board.

I have two codes showing on my obd monitor- one for EGR valve insufficient flow and one for PCM ROM error.
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