2000 and 2001 are prime years for the TSB that is very well covered in this write up
http://leckemby.net/windstar/windstar01.html
As far as head gaskets.....1995 3.8L had issues.
This was corrected starting in 1996.
HOWEVER the lower intake manifold gaskets were a problem after that.
These leaked coolant into the intake, where it was then drawn right into the cylinders.
A head gasket job includes new lower intake manifold gaskets.
If you do not have to add coolant to the system from time to time, then this is not a problem.
The 1999 and newer Windstars used a electrical actuator for the IMRC (Intake Manifold Runner Control) system.
Above a certain RPM (like hard acceleration) A extra port per cylinder is opened up in the intake manifold.
A combination of length of the intake manifold run and the extra air intake gives the vehicle more power.
At lower RPMs (including normal driving) only 1 port is open in the intake for each cylinder.
If both ports are open, the engine does not run as well.
Also, if the extra ports are open for the cylinders in 1 bank and closed for the other bank, this will also cause the engine to not run as well.
It is common for the nylon clips that connect the shaft for each of the 2 rods (1 for the front bank of cylinders, the other for the rear bank of cylinders) to just fall off.....leaving them not connected to the control actuator.
If this has happened, the best position to fasten them in is the closed position.
1999 and newer windstar seems to be more prone to developing cracks in the epoxy body of the coil pack.
The coil pack contains 3 coils, each firing 2 cylinders.
When a crack develops in the epoxy body, the high voltage can arc through there and cause a misfire.
The best solution if you suspect this is to replace the coil pack.
The EGR system SHOULD be always closed when the engine is at idle.
The EGR ports clogging causes problems......the reason being that the ports clog closest to 1 side of the engine first, progressing to the other side.
Then 1 or 2 cylinders get all the EGR flow and are starved of oxygen, causing the misfire.
The EGR flow sensor, called DPFE, is also a common fail item for EGR issues.
Also...verify the vaccum line to the EGR valve at both ends to make sure that it is connected.
Good news is that the EGR valve itself is not a common failure and is unlikely to be causing your problem.
The EGR valve control solenoid.......which is what the other end of the vaccum line the connects to the EGR valve, connects to SOMETIMES can fail......there is a little air filter on it (vaccum driven valve) that can become clogged, causing it to malfunction. There is normally a SMALL amount of vaccum in the line.......but not enough to open the EGR valve until the computer calls for it....and activates the EGR control solenoid, causing significant vaccum to the EGR valve......opening it.