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I have a '00 XLT w/v6 SOHC. It ran well for the first couple years, but then it started missing. First, on 4, then on 5 and back and forth. The wires and spark plugs have been replaced and the fuel system cleaned. After changing the wires, it was fine for about a couple months but, it's back.......The thing is, now it's worse. Before, it would miss only while warming up. Now, it has continued to miss!
Why did the wires fix the problem for a while? Why is the problem worse now?
I will venture a guess here based just on the information supplied. If you replaced your plug wires with a generic, economy brand there is a good chance those wires have disintegrated already. The intense voltage generated by these ignition systems will rapidly erode the conductive material within the wire, causing ever increasing resistance to the plug. This causes misfires of the type you describe. The middle plug wires, being the shortest, erode the quickest.
If you have access to a meter, you could purchase a new set of Bosch or Motorcraft wires and one-by-one, remove the existing wires comparing their resistance with the new wire. If no appreciable difference, return the new wires because this is not the problem.
Like I say, a guess, but I had a similar experience. To have this happen within a few months is rather uncommon but all your symptoms point toward this.
Actually, I took it to someone to get the wires changed (I've read on another thread how it could be a chore). He had me go to the dealer for the correct, more reliable wires (I got them cheaper than he could have because of his mark-up). They charged me $100 just for the wires, and he put them in.