Sounds like you indeed have a blown head gasket. If water is appearing in the oil, then that's a classic tell-tale sign of a damaged head gasket. There are a few ways you can check for blown head gaskets - 2 of which have already availed themselves to you.
1: Water in the oil. Sometimes this will turn the oil into a sort of "chocolate" like color as the coolant mixes with the oil.
2: Coolant disappearing from the overflow tank and radiator. Unless there's a leak somewhere, then it's getting sucked into the crank case.
You also mentioned that the engine is running rough. If that's the case, then this too is another possible symptom of a blown head gasket.
Your best option is probably taking it to a mechanic and have them verify that it is a blown head gasket. Unfortunately this can be an expensive repair, so you'll need to weigh the pros and cons of repair. Either way, good luck!
My check engine light came on, and it read that the transmission pump was bad. I know enough about most cars to know when the pump in a transmission is bad. It would go off and come on saying the same thing. It was a bad front bearing, causing enough drag to allow the tranny to think wrong. 1 hour of work, and it went out.
I don't understand some of you. If you have a check engine light, get off the internet, and take yourself to an auto parts store. Tell them you need your vehicle scanned if you do not own an OBD II scanner. They are more than happy to come outside and run it for you if you do not have the know how, as you will generally need to come inside after the parts to fix it. I hope this helps.
Oh, BTW, vehicle maintenance is VIP if you want it to last. I have a 99 Windstar with 198k on it. I overhauled it at 195k and it runs like new. The only transmission problem I have had is the front pump seal exploding on me recently. I am guessing it is a TCC problem more than an internal gearing problem. Guess I will know when I pull it off the van tomorrow. Good luck.
FYI, that sounds more like an electrical problem. Most mechanics do not want to toy with repairing a transaxle, if they are even capable. Usually unless it is seized up, it can be repaired. I have been an honest diesel mechanic for over 12 years now, and will be the first to tell you that the words transmission or transaxle directly translate to "buy a new one" to most combustion engine mechanics. Hope this helps you in the future :)
The Windstar wasn't one of Ford's stellar models, however with proper care they were generally a pretty reliable vehicle.
As some commenters have pointed out, nearly all auto parts stores will be glad to scan your check engine light codes free of charge and tell you what problems are indicated.
Often these lights are hyper-sensitive and come on for little or no reason. The check engine light has been on in my GM vehicle for seven years, and on my Ford for three years. Both codes show problems that in no way affect any aspect of the car's reliability or performance, so I ignore them. Our local inspection stations don't require unlit check engine lights, because they have nothing to do with safety and the emissions check is a totally separate procedure.
Often previous maintenance procedures can adversely affect a vehicle. Many people don't realize that OVER-maintaining a vehicle can cause as many problems as a lack of maintenance. I always advise strictly following the vehicle owner's manual. The people who wrote it designed and built the car. They know far better how to maintain it than a greedy shop or dealer who just wants your money.
My 99 3.8 Windstar is fine with 205,000 miles on it. I may replace the rear hubs myself. They run about 43 bucks each... so low it's not worth messing with pressing the bearing out and in.
Change the oil every 5000 miles.
Flush the tranny - change air, fuel filter & plugs - add fuel injector cleaner every 30,000 miles (filters sooner if needed).
Change the wires every 60,000 miles (cap rotor) to 90,000 miles (direct ignition).
Most will go 200,000 or more if you take care of them. I always add more tranny fluid than the normal line on trannys, but not a lot more. Always check all fluid, tire air pressure etc every week or 500 miles (whichever comes first). Keep your eye on gauges, and shut it down if something goes wrong and investigate before restarting.