2002 Dodge Intrepid Possible faulty computer

Well, fella's, I got a good one. I have a 2002 intrepid with the 3.5 SOHC, just shy of 70k miles. My check engine light came on (car ran fine at this point) and when scanned gave codes for defective oxygen sensors (upstream). I replaced both, and did the spark plugs while I was at it. The car only started running rough though! Double checked the sensors, and then even replaced the new ones! Looked on the internet for what else may be wrong. I was influenced to go ahead and replace the upper intake manifold gasket, but it was not the problem. Took the car to a mechanic who advised me to let him change the plugs (he claimed that the bosch plugs I used don't work as well as Champion plugs), and do a fuel system cleaning. It still ran rough. Put a can of fuel injector cleaner in it, still ran rough. The car will miss, stutter, and stumble (sometimes at a stop, sometimes while accelerating). Before allowing the first mechanic to start replacing fuel injectors, I got a second opinion. The second mechanic suggest that the computer needs to be flashed, and can only be done by the dealer. The problem there is that the last time I took the car to the dealer, they were unable to establish communication with the computer (this was when wal*mart destroyed my key trying to make a copy). Walmart refused to pay for the repair, and I am scared that it is coming back to bite my behind. What can I do?