2000 Windstar, Strange NEW Problem

Gentlemen:
My Windstar suddenly started doing something new......it runs GREAT when I first start it up and it's cold. As it begins to warm up, it starts running like "crap".
Next, while driving, the "check engine light" (which of course is always on, no matter what I do or replace) will start BLINKING! (never saw that before). While the light is blinking, the engine runs like "Super Crap"! After a few minutes and/or miles, the light will stop blinking and the engine will return to it's "normal" running like crap (as opposed to Super Crap)

Any Ideas? (other than replacing the vehicle)

A blinking CEL is an indication of a condition that can damage the catalytic converter if you continue to drive the vehicle.
The most common issue is a misfire.......P030x

If the misfire is caused by a spark issue, then the gasoline is not being burned in the cylinder that is not firing.....and that gasoline is now going into the catalytic converter and burning there......which will make it cherry red.
This will damage the catalytic converter.....to say the least.
Spark plug wires, bad coil pack, or defective spark plugs are the common spark issues.
Coil packs seem to be more problem prone on 1999 and newer windstars, but you vehicle is also at the age were spark plug wires and spark plugs are due for changing (if not already done).

If the misfire is due to lack of fuel, or a vaccum leak (too much air), then it would not be putting raw fuel into the catalytic converter.....but still set the same code (misfire) and give you the blinking CEL.
You could also get P0171 and / or P0174 which indicate a "lean" condition....almost always due to a vaccum leak.
On the newer windstars, dirty fuel injectors do not seem to be as common, but fuel pump issues (weak or intermittent fuel pump, fuel pump relay, fuel filter) and vaccum leaks are the common issues.

Another cause of misfire is clogged EGR ports in the lower intake manifold.
There is a port, a small 1/4 inch hole for each cylinder in the air intake in the lower intake manifold.
They develop a clump of black soot......a combination of exhaust particles and oil vapor right at the end of the port......with the ports on the driver's side clogging more....and closing off first.
This leaves 1 or 2 ports on the passenger side open.....getting ALL the EGR flow, which does not have as much oxygen.
This causes a misfire on cylinders 3 and/or 4 (P0303 and or P0304).
The solution to clogged EGR ports is to remove the upper intake manifold and clean the deposit from each port.

I would have the codes read (most auto part stores will do this for free) and get the actual numeric code.
If you have a P040x type code, it could be clogged EGR ports or a defective EGR flow sensor (aka DPFE....Differential Pressure FEedback).

It is easy to test to see if the EGR system is causing the misfire.
As a TEMPORARY test ONLY.....remove the vaccum line from the top of the EGR valve and plug open end of the vaccum hose.
Take the vehicle for a drive and see if the rough running happens.
If the rough running STILL happens, then it is NOT caused by the EGR system or the EGR ports.
IF the problem does not happen, then the EGR system is the cause of the problem.
Do not forget to reconnect the vaccum line to the EGR valve after the test.
This test should cause a P0400 or P0401 code for lack of EGR flow.....since you have disabled the EGR valve from opening.......so get your codes read BEFORE this test.
The EGR valve is quite reliable.....the 2 common EGR problems are the DPFE and / or clogged EGR ports...

Resolved: I had P0303 & P0304 (Misfire plug 3 & 4), along with P0171 & P0174 (O2 sensor) via free read at Auto Zone. It was the Coil Pack. Must be common failure if it's 3&4 on all these codes.

2002 Windstar it's mid engine, just behind the intake; follow the spark plug wires. Very, very easy to change, only need minimum skill on cars. I'd buy the replacement first so you have it right there when you pull the old one. Look at the new one to see where the 7mm hex bolts are. First reach in (A little tight, but arms will fit around both sides of engine) an undo all three hex bolt, it will make it easy to disconnect thin wire connector and plug wire if you can move it around. Then unplug thin wire connector, I had to use needle noise in order to pinch the little tab that released the plug. Move the new coil back there pune plug one at a time, plug into the new immediately to get the righ socket. Pull old coil out when done. Plug in the thin wire connector. Move new coil over mounting screw holes. I had to unplug a few wires one at a time again to get them to lay right in order to get the coil to sit right. Put in hex bolt Very Very lightly! only snug, barly snug, or you'll bust it. Start the car and Vrrroom! runs like it's brand new! I had codes P0303, P0304, (Misfire 3&4 plug) from the free computer read at Auto Zone- along with P0171 & P0172. All codes gone after this coil replace. I don't know why Ford put such a crapy part that fails on there cars. Runs like a champ now. Good luck. Part $65 at auto zone.
Tim O.

Forgot to add above coil pack: engine was chugging with no power. occasional poping noise in exhaust. Wouldn't rev enginge without acting like gonna stall.