I'll guess I'll try to be clearer on this. I don't think the running rough problem is related to the smog pump. Just the rich smell. If you have cats in place, you SHOULD have a working smog pump otherwise the cats are not going to work properly and will eventually clog causing an exhaust restriction.
I have a CompuCam 2040 (E303) and have no problems with vacuum or brake boost. I also have a 351W which is why I may have more vacuum.
Gray87GT, the circumstances you're testing are so unusual so I guess we still need a little more information. When you're at 2000-3000 rpms with your foot off of the gas, is the clutch in or out? Since it's at 2000-3000 rpms I suppose I can assume that it's out and you are using the engine to slow you down. This is the point at which vacuum is highest. (That's just an FYI, but not necessarily a cause). If your TPS is off in the high range (Mine's set at .98 volts), your ECM may think that you're at normal cruise and opens the EGR which would make it run crappy. Magazines say that closest voltage you can get that is under 1 volt is best. If you're at .999 and you tap the throttle, that may cause the false reading by the ECM.
To test this theory, disconnect the EGR vacuum line so that the ECM can't open the EGR. See if it still does it.
Crap, just noticed that you have the EGR blocked, but I'll leave this for the other people to try. It is still possibly related to EGR, though. Do you still have the EGR spacer with the EGR valve hooked up to avoid EGR codes? If so, the ECM may be adjusting fuel values thinking that EGR is present. If you don't, then maybe your engine doesn't like the transition from engine braking to slight throttle. I'll check to see how my engine responds to this because I've never actually done this before.
Another thing you could try is to bump your TPS down a little if it is high or on the edge.
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351W 89 Mustang GT Convertible