I found a Internal company Service Bulletin for this problem on trucks built from January 2007 to Present, may be worth a look:

Complaint: Intermittent to Hard communication codes such as, but not limited to PO3,PO4,PO7,FO4 & FO7

Cause: The diagnostic connector under the cup holder has a possible build up of corosion that is shorting across the CAN lines. This causes the VCM to see false communication signals and generate these codes.

Correction: Clean connector with electric parts and contact cleaner, Then remount under the dash in a horizontal position to prevent moisture from collecting in the boot, if corrosion cannot be cleaned out enough to prevent codes the wiring harness must be replaced at this time.