I've heard of some isolated incidents where a CEL can come on after a re-fuel of E85. It's somewhat uncommon though. Depending on the dealership, I've heard mixed signals on what the real fix is. Some have mentioned a re-flash of the PCM to take care of it, others have simply cleared the code and not had it come back, and yet another told the customer not to use E85 if a CEL came on during its use. The last one gets me a bit steamed. It was probably a newbie in the service department that didn't know his arse from a hole in the ground, but it still isn't the answer to give someone that bought a FFV and planned on using it to run alternate fuels.
I'm pretty confident that a re-flash of the PCM will solve your problem if simply clearing the code doesn't. Heck, there's quite a few non-FFVs around this area that are running E85 with hardly any issues whatsoever. One of my mechanics has an old '91 Olds Cutlass Ciera with a 2.5L 4-cylinder and he's been running it on straight E85 for some time now with no Check Engine lights ever coming on, and no fuel system problems to speak of. In fact, he claims it makes more power on E85 than it does on gasoline. Only gripe he has is that it's a bit rough idling when dead cold. Once it warms up, it runs fine. I've got a way to fool the ECM on that car into fattening up the fuel curve a bit but so far he hasn't tried it. Basically, just hooking up a small potientiometer into the coolant temperature sensor wiring to give the ECM the illusion that it's much colder (you can default it to -40° this way), and it will then dump more fuel on a cold start. Once warm, just turn the dial the other way, and it will lean back out and run in closed loop operation.
Replacing the fuel filter is probably a good thing to do, but generally, if it's getting plugged up, you'll start to have driveability problems regardless of what fuel is being used. I'm guessing that my Explorer had a diet of regular gasoline up till I bought it, just based on where the previous owner lived there's no E85 stations within 50 miles or so. The day I took delivery of mine, I went and filled it up with E85 and have been running it every tank since with no problems whatsoever.
