There is a sweet little tool made by Thexton, , . When used according to instructions, it will provide hard codes, continuous codes and also utilize the feature of dynamic testing which is present within the ECA of your vehicle. The last time I checked the cost was under 25 dollars. It is only for OBD l systems. The dynamic testing will run the engine through a series of tests and will provide codes of any malfunctioning areas. It does this by providing blinking of the LED on the tool.. It will check out the function of the EGR system for you and if any problem will provide the blinking light code.
There is a wealth of info in the Ford OBD l system that a lot of folks are not aware is available there.
You might try, Tool Source 1-888-220-8350

 

Some things I would check, make sure you throttle body is clean, the throttle blades(also are closing all the way) and throttle cable are not sticking. Hopefully you have not distrurbed the "forbidden" screw called the hard stop screw on the throttle lever. It should never be touched.You have no vacuum leaks. Pull the vacuum line off the EGR, plug it and see if anything changes. You should not have any vaccum on a cold engine or when it is idling. If the EGR were stuck partially open, it will also affect the engine when warm. Any opening of the EGR at idle will cause it to nearly stall or stall out completely.When these trucks get this old with weird problems, I always CHECK the ECM. A common problem is the three electrolytic capacitors on the circuit board will bulge out and leak. You can disconnect your battery and pull the cover off the ECM to check. Stop replacing things, test and verify your parts. By changing things blindly, you could introduce additional problems.

 

Even if the EGR is new, make sure no vacuum is being applied at idle like raski implied. If the EVR is not closed and is switching/open at idle, as soon as the engine is strarted vacuum will be applied and open the EGR.

 

Just checked this morning.egr doesnt have steady steady vacum at all just kinda pulses against your finger?

 

How does it idle with the vacuum line disconnected?

 

Idles the same with or without the vacum.

 

Since we are throwing in everything except the kitchen sink, what about the oxygen sensor?
If you have a lazy o2 sensor , it takes a while for the injectors to catch up and when they do , it overfuels.producing increased RPM, then when the system gets a late notice it reduces the injector on time to correct a rich condition and now it finally slows down repeating the cycle.

 

just replaced the oxygen sensor.cold start and idle are alot better but warm start and idle seem worse.

 

just did a compression test on the engine.Highest was 150psi Lowest was 125psi.Thoughts?

 

I have seen worse numbers than those and had no idle problems.
There are certain functions that are controlled when cold and others when warmed up.
Generally the ECM controls fuel with preprogrammed info when cold , then when a few conditions are met the ECM controls fuel based on system info rec'd.

It could be one of the pieces of info rec'd , the ECM itself, or some other possible mechanical problem.

What kind of problem is showing up on warm starts?.
Where did you purchase the oxygen sensor?