I don't know if you have the alternator fuse on your '98 or not.
My only experience is with my '96, and it is fuse "T" on mine.
So I could have sent you looking for something that is not there.
As far as coolant, I would replace the radiator cap......with a normal one....not anything fancy, but at the correct pressure rating for your year fo vehicle (I don't know if they changed that from year to year).
Also, clean the seat in the radiator neck that the cap seals against.
My cap would not keep pressure.....and I could get it to work for a short while by cleaning the filler neck.....a new cap solved the problem.
It is sounding like the cap may be leaking.....as your radiator was low...but did not draw coolant in from the overflow tank.
I did notice that my '96 did not have a clamp on the hose from the overflow bottle, where it connects to the radiator by the cap.
You might want to check and see if your hose is loose at this point.
If it is loose, then you might want to put a clamp on it.....but don't tighten it real tight.....just very slightly snug is plenty good enough.
I would also get a oil sample kit (free) and send a oil sample in for testing.
They will tell you if you have coolant getting into the oil.
I have used this place
http://www.blackstone-labs.com/
They have always gotten back to me real fast.
I get an email within a couple of days of sending the sample to them.
They will also call you if they find something important to pass along.
Then you get a paper copy in the mail.
This is WELL worth the small fee they charge to test your oil.
I take the sample when changing my oil.
The 1995 3.8L windstar had head gasket issues, but they made improvements for the 1996 model year, and again mid-year in 1997.
I heard the head gasket routine plenty of times with my '96......and it was only the lower intake manifold gaskets.
Of course, if you have the head gaskets replaced, the job includes lower intake manifold gaskets, so IF the job is done correctly, your problem would be solved....but for more money.
I am one to leave the head gaskets alone if they are fine, particularly given the fact that they are NOT a high failure item on post 1995 model years.
Lower intake manifold gaskets have been an issue with a number of different vehicles from different manufacturers in recent years.
FORD did make improvements in the replacement gaskets for the lower intake manifold and the front cover to address the issues that caused them to fail in the first place.
Also, the Bar's brand of stop leak will NOT clog your heater core.
There may be brands that do....I do not know...but Bar's makes the stop leak that the manufactures add at the factory on some vehicles.
The hot water is always flowing through the heater core whenever the engine is ON.....so it is not just sitting in there when the heat is not on.
There is a blend door that controls how much air flows over the hot heater core....which is what you adjust when you adjust the temperature setting.
Having the coolant always flowing through the heater core prevents the issue of it being a place where the coolant sits and lets stuff settle out and create a clog.