Windstar 2003 check engine light, no code

My Windstar has 91,000 miles. Several months ago, with about a quarter of a tank, in rain, the check engine light came on, blinking. Engine was missing. My mechanic put new ignition wires on. Several weeks later, similar thing happened, but stopped after about 2 minutes. 3 months later, 1/4 tank of fuel, heavy rain, again the light was on blinking. Took it to my mechanic but the light turned off by the time he connected his computer. A code showed a problem with the 3rd injector. Plan was to replace it. After I left him the light started blinking and I filled the tank. Light went off, then came on but not blinking. I took it to him 2 days later to repair. But, no light, no codes, running like new! I wonder if there is a problem with water in the fuel? Any ideas?

Water, or other contaminants, in the fuel would cause a miss in all cylinders. That #3 cylinder could be misfiring, a little, all the time; but, not misfiring enough to cause the check engine light to come on.
Misfire can be caused by a number of things. It could be fuel injection, and it could be spark caused.
Since the spark plugs are a real pain to change in the Windstar (ask your mechanic about those -)*&%$%#@!!^ spark plug wires), ask your mechanic to change #3 spark plug. If he’s willing, it’s time (mileage-wise) to change all the spark plugs.
Your mechanic should listen to the clicking of #3 fuel injector, with a mechanic’s stethoscope or finger tip. He may have other tools he can use.

It confuses people when you have two post on the same problem.
You can link the posts, like this:

Fuel level is probably coincidental,and fuel contamination probably not relevant either. Rain is a key condition here. Check the coil block for cracks in the housing right at the plug wire tower for the # 3 plug wire. Fractures in the housing get wet when splashed, especially in heavy rain with standing puddles. The spark then grounds out and you get a dead miss in the #3 which eventually will abate as heat and time ( say long enough to fill up)dry it out.
Ford will tell you its a problem with the plenum gasket ?!($438.00) but no explanation why it only happens after driving through standing water, usually at higher speeds. Because there isn’t one -that’s not the problem. Then they’ll tell you its a broken plastic fitting in the fuel rail ($382.00). Its not. Then they’ll try new plugs and wires (twice, less than 1 month apart -about $108.00 a whack). That will work as long as you don’t drive in the rain.
Finally, If you insist they’ll replace the coil block. I just had another one installed today, as a matter of fact, after the Windstar stranded my wife driving alone in rural Iowa in a thunderstorm. ($170.00 Tow and hotel bill until it was dry enough to limp back) Ford will also tell you that there is no design flaw leading to regular and predictable failure. Perhaps they’re right about that last point, but the chances that my wife will agree to buy any other Ford, ever, are about the same as my success rate in getting this problem acknowledged, diagnosed, and fixed. Not bloody likely. Too bad, too- I’ve owned Fords for 20+ years. After this latest one fails I might be able to offer some insight as to whether its a thermal fracture, or a mechanical one- say, overtightened mounting bolts. I’m pretty confident I’ll have the opportunity to do the research, especially since there’s no design flaw… I wish you better luck than I’ve had . Hope this helps.