Regarding my suspicion that simultaneously providing both usb power and external power to a mega2560 can damage the 16u2 (usb controller chip) I am now removing transistor T2 from the mega2560. This transistor is what allows usb power to be connected to the 5vdc bus. Removing it totally prevents usb power from being used.
Note that you cannot just clip the 5vdc wire (or an unpowered hub I think) because the usb power is applied to the 16u2 and is used to power an internal component which is used to provide power to the data lines. I tried this first, and it resulted in very very shaky usb connections. Sometimes it would connect, most times it wouldn't.
But removing T2 removes usb power from the 5vdc bus AND yet still allows usb communications to work properly.
to be continued...