I had the same problem on my 2001 taurus. I changed plug wires, it was a cheap tuneup, and plugs. No go. I then proceed to price out some new injectors because thats what I narrowed it down to. I put in some stp injector cleaner and ran it for a couple miles and it went right back to normal. Ever since then I have been using Ammoco fuel and she has been liking it. Before I used the cheapest of the cheapest gas. I know you said you tried fuel injector cleaner. What type if you remember? you might even try some octane booster. I have read, in the past, about some muscle cars in the 80s and their carbon deposits. Running higher octane fuel with some booster seemed to help many knock that carbon loose. In our case it would be a clogged injector and not carbon but a similar idea.
I would try to narrow it down to which cylinder is missing. You can do this by pulling a plug on the "distributor", don't know what the newer robot boxes are called, and start the car. If the car runs worse that you know that that cylinder is firing. Keep doing this method for each cylinder until you come to one that makes the car run the same as it would with the missing cylinder. If you hear/feel no change then that is the cylinder that is missing.
The reason for this method is because when you pull a plug it will shut down that cylinder. When that cylinder shuts down it is "missing" which will make the car run rough. When you pull the plug of the already missing cylinder then the car won't change at all. I will still run like it did the miss to begin with. By pulling the plug on a firing cylinder, you are create 2 misses which will obviously make it run worse that 1 miss. Hopefully this makes some sense to you. It is also the barnyard way to diagnosing the problem. You may endup having to replace the injector on the "lazy" cylinder and that is how I found mine.
Good luck!!
Another Pete
