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k9guy, I feel your pain bud. Going to the Ford Stealer can suck extra too... Be weary, I know these things are always different, and I haven't gotten back to find out what my deal is yet... but here's the story, so maybe you'll get some guarantee from them before you buy a new ECM.
My engine was running rough... similar to yours. Slight stumble at idle, jumpy and crappy at lower RPM's and when steady at 1500ish... if I punch it, it'll hesitate the go balls out and run good... if I'm cruising on the highway at 2000 RPM, it runs good.
So... it got scanned and showed 6 and 8 injectors were bad... so I had them rebuilt. But before that, we changed the oil and filter and it cleared up for a day or two, ran like a dream... have no clue why? New injectors, fuel filter and it ran better, but not perfect.... he scanned it again, couldn't figure it out.
We swapped the ECM with a unit he had that had been pulled from another truck... it had a 100hp reflash done to it.... bam the truck ran like tits... it spun 36 inch tires on dry pavement and chirped them going into second... big smiles on my face. My truck ran like a dream for another day.... and has progressively gotten worse since.
So, this swap and pray stuff can get spendy. I'm thinking I may have a harness/wiring prob... maybe air leak in the fuel system... hpop.... I've been researching and not sure what to think.... guess my point is, it maybe something else throwing the computer off and maybe you can find someone to reflash it or swap one out to test the mechanics theory... you'd think the ford stealership would do that before they clipped you for a new one...
Good luck with your woes k9guy....