In the Car Talk column on 1/3/2016, it sounds like Lynnette’s 1991 Honda Civic wagon was experiencing very similar symptoms to my wife’s 2001 Honda Odyssey (189,000 mi) a few months ago. Rough idle, engine almost dies sometimes at stops, groans during acceleration. Additionally, accelerating between 40-60 mph our Honda would feel like it was “loading up,” running rich or in the wrong gear climbing hills. I replaced the idle air control valve, which fixed the rough idle but not the other symptoms. Turned out I needed to reset (power cycle) the ECM and go through a curb idle/rev warm-up procedure so it would relearn the throttle position sensor’s operating range after replacing the IAC valve. I disconnected the battery, removed and reinserted the hazard fuse, then reconnected the battery. Then from a cold start held the throttle at 3000 rpm until the engine warmed up to normal or the electric fans kicked on. Since then it’s back to smooth, strong acceleration we expect from the Honda we love.
All of which probably has nothing to do with a car that is 10 yrs older, different engine, different emissions standards, OBD I. Personally I would not hold an engine at 3000 RPM from a cold start to warmed up even on a new engine, much less a 25 year old one. Then again it’s not. my car, you can give the above a try, let us know how it turns out.