Hmm, if the computer won't connect to a scanner, it could indicate an issue with the diagnostic module which warrants replacing the unit. However, it's not impossible that the scanner used was indeed unrecognizable. My folks had an '04 Expedition that had a misfire and they took it to a dude's shop. He had one of those multi-thousand dollar scanning tools and the Expedition wouldn't recognize the scanner. However, I went and hooked up my two hundred dollar scanner and it worked just fine...
Have you switched the plug wire with a different cylinder? If the misfire moves, you've found your problem.
Also, have you re-routed your plug wires via the TSB? If you're using 10mm aftermarket wires, this isn't so much a problem, but most replacements are 8mm and they tend to crossfire if they run parallel to each other.
Finally, what plugs are you using? Anything other than plain ole copper tips can cause plenty of running issues on these engines.