Interesting I am having a similar problem with my 99 2.5L cougar. I don't exactly know what you mean but stutters but my car doesn't feel like it wants to go below 3000rpms. The car jerks like 2 or three times and then when the secondaries open up the car runs like a bat out of hell.
I pulled my exhuast off and found that my hi flow sho shop cat was all eaten away to about a chuck the size of my fist. I knew it was broken but I didn't know it was that bad (oh that is my second hi flow cat to

). I got the misc chunks out, changed the oil and put the stock intake back on. No dice, the car runs the same. I am going to get a S-AFC next week to see if this will help. I know it is running rich because that is the only reason the cat would be eaten away so bad. The car must be dumping fuel right into the cat.
This is why a 3.0L swap will take place this summer.
Later,
Chris