Spitfire you say "EGR system (all of it)" but did you clean the port leading to the air intake from the EGR, behind the Throttle body? I've been following your thread here as I have what sounds familiar to your problem.
I took off the EGR to find the port leading into the Upper air intake was blocked SOLID! At the EGR end and into the EGR was a mass of slimey goo. About an inch in the goo turned to hard carbon and futher into the mass(2") was solid carbon. I'll attempt to add a picture.
I also ended up replacing the EGR with new as it was in no way cleanable. I put a vacuum to the old EGR and could see very little movement compared to a new one so it was replaced.
The upper air intake on my truck was black inside.
I have started with a can of intake manifold cleaner. The type you use whilst the engine is running. Reving up the engine and spraying directly into the Upper air intake. By my second can of intake cleaner I noticed a huge difference. I was spinning my tires from a stand still,(not my norm). Also added a double dose of Lucas Injector cleaner to the fuel tank.
On a daily basis I'm getting better performance.
Just a note... I spoke with a Ford mechanic.
When he looked at my truck first thing he said was,
Spark plug wires
Clean the Throttle body and intake good.
replace EGR
replace Air Bypass Valve Assembly
Fuel pressure check should be 30 - 40psi
(Fuel pressure on my truck at key on= 40psi, Engine running @ 36psi)
I live in the Pacific Northwet (west)
The 2.9, (especially the early 2.9s) had a common problem with the fuel rails rusting from the inside, very much like the cheap portable BBQ burners. Look at the fuel rail and look at a cheap BBQ burner, now tap the rail...
Like I said earlier in this post I'll try to post a picture of my EGR, but being a noob may not be able too.
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Hey I wanna thank everyone for helping Spitfire here it gave me a place to start my search. This and other posts...