OK here is the deal! my 1997 F-350 "Ole Whitey" got a TS 6 position chip installed in her about 6 weeks ago. Ran better than ever

ok so i have to drill the hole for the selector switch for the chip! I was at a Buddies house and used what was available drill-bit wise! needless to say i used too long of a drill bit and got into the wiring harness under the dash and created a No-start situation! I fixed repaired all the wires still nothing! "Checked ALL Fuses!" no wait to start light i tried everything to my knowledge and power to DIY and it was a no go! i took it to the

House! They say it needs a PCM! I said OK but informed them of how the truck got there in the first place! So a month go's by and i get the PCM Re-manufactured from Oreillys! man what a wait! so now I get a phone call from ford saying My truck starts/runs fine except i have a check engine light and none of their scan-tools/equipment can communicate with the PCM! @$90
pr hour Im biting my nails! What would cause such a thing? why/how can a truck run just fine but not be able to communicate with the PCM? I'm Damn sure it isnt a fuse! Maybe someone who reads this has had a similar experience and could share! Thanks Ryan