E-04-F04 mean the ECM is not communicating with the VCM. Check to see that you have battery volts through the relays to the ECM. Also check that you have a good ground connection. (by the left step) If all is good and the relays don't come in, The ECM is bad.

If you do not charge 12.3+ vdc at idle with lights on (without increasing the rpm of the motor/alt), I am still of the rather firm opinion that you will find either a bad ground or a broken cable (inside the insulation), my bet is the large cable leading to the back of the alt has a break inside the insulation. But the ground leads are a close second.
If this truck is an "LPS" rated version, then you may have bad (usually the positive side contacts) contacts inside the mechanical/electrical isolation shutoff switch assembly on the positive side, and it is able to carry a light load, but dropping out load when loaded up. At idle, when just started, without increasing the rpm of the motor/alt, use a battery load tester and see if the volts stay above 13 v when loaded for a few seconds.
This may also be the diode set inside the Alt having gone bad (especially if it is a sealed alt that has been rebuilt at a local re-builders). I have recently stopped trying to have the sealed Alt rebuilt locally, and for now I am only replacing the sealed (LPS) version Alt with factory new Alts, (not even Promatch rebuilds) as the diode pack that "looks" to fit has had repeated failures (for me) to the point that the local re-builders have given me my money back and declared they can not rebuild that Alt. (yet). If you want my guaranteed fix, you would replace the eye at the end of the large cable to the back of the Alt, replace the LPS shutoff switch assembly [if so equipped], replace the alt with a new (not rebuilt) unit and replace the battery with a new battery, since it has now been run dead a number of times. If you still have this intermittent failure, I would change the 2 wire plug connecttor in the back of the Alt.
You can beat me up in public (after waiting in that rather long line of people who want to beat on me first ;-) ) if that does not fix it for you.
If you still want to change the vcm or ecm, knock your self out, (don't let -me- stop you) but if you do, and it it fixes or changes anything, please come back and let us know. (if it _fixes_ this problem for more than 2 weeks, I promise to be amazed, and will remember what it was that you did that fixed it)
I would have also mentioned a waterpump going bad or loose belt, but since you offered up the 14.6vdc charge rate, I figured your belt was tight

12.8 volts at idle,lights on.i'm thinking i might have a bad ecm or vcm,i did not return to the cust. yet for troubleshooting

how many volts is it charging at idle, right after start up, withOUT having touched the accel pedal? (ONLY having idled, never hitting more than 900 RPM, with headlights on [if so equipped])

battery voltage is good,alternator is charging up to 14.6 volts.i also cleaned out the ground connection at left step rail.seat switch and wiring is also good.did not check the meterpanel area yet.will return to diagnois vcm wiring and i/o signals

just a w.a.g.
seat switch wiring? bad connection under the dash? bad ground or bad alt connection. a low battery, barely getting a charge will toss up weird intermittent codes like that.
does it have the sealed alt? (LPS rated truck)
Closely check the connections to the alt for a broken wire inside the insulation.
what voltage does the Alt put out at idle? under a load at idle? (Lights on?) what is the battery voltage at rest?