well, lets go back a step and take a look at some options...
1) does the truck run fine if you take the chip out? if it does, then your ecu is fine (though the contacts that you had to clean on the ecu itself may be damaged.) if the truck doesnt run fine without the chip, thats not good.
2) youre getting the same problem with both chips, so its probably safe to assume that you didnt get 2 "bad" chips, and that something is shady with the connection between the chip and the ecu (assuming that the truck runs fine without the chip.)
3) i would guess that the connectors on the ecu that you had to clean with the supplied scour pad are screwey, or maybe theres some foreign material/dust/goo/residue or something else on the contacts on the chip itself.
if the contacts on the ecu are messed up, um, i dont know what to tell you. the only way to rectify that might be to get a new ecu (and if it were me, i would just get rid of the chip and leave the ecu alone.) maybe you could take some pics of the contacts on the ecu and post em here? they shouldnt be scratched at all; when you clean them, if metal shavings start coming off, you scrubbed too hard, too much.
one thing that people dont understand is that putting a chip in your vehicle is actually a pretty serious mod. most people think, "200 bucks for plug and play power", and just throw it in and thats that; but stop and think about what the chip is actually doing. its not as trivial as drilling some holes in your airbox; its feeding different information to your truck to make it run differently - not the way that ford intended it to run (even though its generally a safe mod, theres a reason that ford doesnt warranty it.)
jason, heres what i would do. take some pics of your contacts on your ecu and post them here (i know thats a PITA), see if anyone thinks they look damaged. if theyre damaged, get rid of the chip, and drive the truck without it. if theyre not damaged, maybe someone else will have some advice for you. no matter what happens, always keep in mind that the truck will run fine all the time without the chip - it all depends on how much aggrivation youre willing to deal with to get the chip running right in the truck. it might not be worth it, and maybe you should just ditch the chip entirely.
oh, not to be too obvious, but did you contact superchips about this? what did they say? im assuming they didnt have too much advice since they just replaced the chip for you.
good luck.
