It seems that you replaced the UIM over 7000 miles ago. Is that correct? If so, have you gotten another CEL since you replaced the UIM? Also, did you check the EGR passages on the old UIM to see if they were clogged when you replaced it?
If you haven't received another CEL and the EGR passages on the old UIM were clogged, then I wouldn't worry about the P0401 anymore.
I also doubt that the EGR system (or lack thereof) would make the engine surge up and down the way you describe it. I had a P0401 and never had that problem.
Sounds like it could be either a MAF (mass air flow), an IAC (idle air control), or a vacuum problem, but it could be other things as well.
When you replaced the UIM and TB, did you put in new gaskets? Also, did you torque the UIM properly and in the right sequence? My understanding it that torque is important on these aluminum manifolds, since they can be bent if overtorqued.
96 Contour SE
Duratec V6 24-valve 2.5L ATX
108,000 mi.
Replaced: crankshaft w/ DMD, EGR valve (clogged), EVR, DPFE, PCV valve, evap emissions hose & tube (cracked), window regulator (broken), LH & RH PCV tubes, UIM gasket (leak), ignition coil
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