not your typical pats/securilock issues

I was doing some welding on the rear of my 2001 ford f150 supercrew. All welding was done with the negative terminal on the battery unhooked (as I always do). When I was done I hooked the battery up, started the truck and idled out of the bay so I could clean up. when I got back in I noticed the Service Engine Soon light was on steady and the over drive light on the shifter was blinking. My instinct tells me the computer is done. Try to drive the truck and it stutters badly and overdrive doesn't work. I scan the computer with our Snap-On Modis and I get 17 trouble codes relating to emissions, transmission, and air conditioning. Knowing nothing of the pats, I buy a computer that has the same code as my original and proceed to install it... The truck cranks with the new computer but doesn't fire. I search the net and find threads here on the12volt about the passive anti theft system and soon realize the flaws in thinking the new computer would run the truck without issue. I have been in contact with the dealership and the say if I bring in the truck and the new computer they can reprogram everything to work together and cut me a second key. I am not looking forward to the bill from this and am wondering if anyone has any suggestions that would cost less then this trip to the dealer? Is there really no way of making this work on my own. I could deal with the pats being disabled/removed. Any help is greatly appreciated.

I know of no way to bypass the security system in that vehicle.  Vehicle computers have chips in them that can be damaged by even static electricity.  I am sure you know now, but always disconnect any control module, and even your radio before welding on your vehicle.  If you are welding close to a control module, I would remove it from the vehicle.  Welding is probably not quite like lightning, but as far as electronic components are concerned, it's real close.  Disconnecting your positive terminal also would be a good idea. 

i really havent heard of any way to bypass this either but it would be nice to know how much your comp. was and what was the charge for reflashing it. i am having problems with my escape and i think my computer is done.