I have a 2003 5.4L with about 57000miles- mainly highway.

Have had the truck since new-not had a single problem until last week when my coolant recovery tank had cracked and needed replaced- I had the repair completed at the Ford Dealer-

I'm driving yesterday and it started missing as if it were running only on about 4 cylinders- it got really bad-then the service engine soon light came up and started flashing.

So I headed home not knowing what was going on-by the time I made it home- the light had went off and it was running better although still missing some.

I gave up for a little while, then decided to take it for another spin- missed a little bit at first, then got bad again- and the SES light starting flashing. But again this time, it stopped flashing and had went back off by the time I got home (maybe a mile or two).

The only thing out of the ordinary that has happened is that I got gas in an out of the way place-could this be some really bad gas causing this or ?? And if so, what could I do to fix?

 

Go to autozone and get your codes read.
If your truck is under warranty you can probably just get it fixed under warranty depending on the problem.

 

When it comes and goes like that, it could be water in the gas.
Try some fuel anti feeze but give it awhile to work by running the engine, because it is alcohol and needs time to combine with water to become combustable.
If that does not do it then the code should be read while the fault is present because the computer may clear them out if the fault is not present long enough.
There are several stratigies for storing codes is why I say read them when they are present because you could see old code history in storage that does not light the lamp because the fault no longer exist.

 

Water in the gasoline is a VERY probable cause for your misfire, and it may not even be a result of your going to that "out of the way" gas station. I happen to know that at any gas station, when a gas truck comes to fill the underground tanks, it can "stir up" any water that exists in those tanks. How the water gets there is unknown, but I always try to stay away from a gas station that is being "refilled" at the time. I know you can't always do this, but it's good prevention. And then sometimes, you just happen to go to one of those gas stations that Moses used thousands of years ago, and you can't help but get water in your gas no matter what you do. Anyhoo, the point is, I would go with Bluegrass' suggestion and try the fuel antifreeze first. And always try use a good quality brand of gasoline. Good Luck!

 

You can still get the codes read at autozone. it should have stored the code since it happened just recently. If the code is only for 1 plug the it could be a fouled plug or bad COP. If its more than 1 plug then it sound like it a fuel issue.

Some misfire codes:
P0300 Random Misfire Detected
P0301 Cylinder #1 Misfire Detected
P0302 Cylinder #2 Misfire Detected
P0303 Cylinder #3 Misfire Detected
P0304 Cylinder #4 Misfire Detected
P0305 Cylinder #5 Misfire Detected
P0306 Cylinder #6 Misfire Detected
P0307 Cylinder #7 Misfire Detected
P0308 Cylinder #8 Misfire Detected

 

You hadn't washed the motor or gotten it wet did you?

Sounds like one or more of the Coil on Plugs is out on your machine.