Hang in there, this is a long one, but I hope to give you all the details you need to shed some light on this!
I purchased a used 2002 Saturn SL1 in April 2004. The car had about 32,000 miles on it at purchase. A few months after I bought it, I started experiencing some random, repetitive hesitation while accelerating, particularly just prior to the automatic transmission shifting around 2000 RPM's. I'd also feel this just about any time the car was going up any sizable incline at speeds under 45 MPH.
I took it to a mechanic who said he couldn't reproduce the issue. Admittedly, it wasn't a consistent thing, and seemed to happen more often once the car had been driven a short distance (a mile or two). The car sounded fine, never appeared to be on the verge of cutting off or leaving me on the side of the road, so I stopped actively pursuing a fix. During regular maintenance and other repairs I would mention it to whatever mechanic I happened to be dealing with, and he would take it for a drive and come back saying he didn't feel anything.
Fast forward to around this time last year. Transmission starts to go out at about 90,000 miles. New (used) one goes in. Transmission is working fine, but this bizarre hesitation is still there, exactly as before. I mentioned it to the transmission shop on a follow-up visit, and again, they didn't notice anything.
New transmission is still doing well, and I recently had a good bit of maintenance work done on the car to resolve a rough idle situation, including a complete tune-up (plugs, wires, fluids, etc). The intake gasket was also replaced. Rough idle was fixed by this. Car's also running on a fresh battery.
Since this repair was completed, the hesitation is still there, just as noticeable as ever (when I'm behind the wheel anyway). However, now I'm also feeling it when I'm driving along on a flat surface between 35 and 45 MPH.
. . . BUT. . .
A few nights ago I noticed that if I turn off the A/C, it clears up. The car performs wonderfully during acceleration, up hills, and on flat surfaces. Turn the A/C on, hesitation starts. The air conditioner works just fine (think "meat locker") but there is a distinct "tug" on the engine when I turn on the A/C, more than there was prior to the last bit of mechanical work. I also noticed that the lights on the instrument panel would flicker ever so slightly while the car is driving rough, almost like an alternator issue.
So, given the strange pattern of occurrences and my mechanics' inabilities to spot the problem, I turn to you guys. Any ideas what might be going on? With 110,000 miles on the car, I was suspecting perhaps an EGR valve issue, except I'm curious about the electrical impact this is having and how the air conditioner might be connected to the trouble.