96 Accord 2.2L runs terrible after warmup.
 

Does the check engine light turn on when it starts acting up?

I would stop by a parts store and have them scan for codes. Your connector is behind the ash tray. Post any codes you find on here, they start with the letter P and have four numbers, like P1234.

Are the maintenance items up to date like the distributor cap, distributor rotor, and the spark plugs?

I will grab the codes and I apologize for the following book but I feel more is better sometimes -

This problem was little progressive in nature. A little history:

The water pump seized up. Luckily I made it to a rest area with just enough tooth meat left on the timing belt to turn the camshaft because it kept running even though I was leaking antifreeze and it was getting hot. I would pull over and let it cool and then drive a mile or two then stop before the temp gauge hit red. Got it towed from there to my house where I began my endeavor. I replaced the timing belt, water pump, plugs and wires. At first it ran fine then it started with intermittent chugging then it sounded as if it were misfiring and out of proper timing. All within a couple days.

I double and triple checked the TDC and Cam marks,
verified compression stroke on #1 TDC
Ohmed out injectors at rest(2 ohms on all)
Checked EGR ports under the valve (Clean)
Pulled vacuum on the EGR diaphragm and it raised with no problem.

Try to imagine- starting it cold, it runs and responds great, can even chirp em in 2nd (it's has an AT). Once the temp get to 40% and the fan kicks on it will not accept any acceleration without chugging, dogging, spitting, stinking. If I downshift (D3, 2, 1) it gets better but it still dogging a bit just masked by rpm. In neutral i can rev it to red and it feels normal but as soon as I put it in gear again it immediately chugs and dags to the point of almost killing. At idle in this condition it smells very gassy, and it idles very rough. I have resorted to adjusting the idle to 1500 in gear just to keep it running. Unfortunately it is 2000 in park which sucks. Any help is greatly appreciated!!

Chad

Does sound like a lazy O2, had to say without testing. They can sometimes be "out" but not set a code, testing can confirm.

In your post you say you checked the ports "under the valve"....Check the Common DIY Threads for pic's of the ports....did you pull the chamber apart?

For future reference, when a car over heats, turn on the heat full blast. This helps cool the engine. You will be miserable in the car, but this will prevent the engine from overheating.

The overheating could have damaged the head gasket, the cylinder head, or possibly the engine. You might want to try (or have a mechanic) do a leakdown test.

Mine acts like it is doing the same thing...just did the same replacements/repairs. I am at a loss as well. Although I dont smell the fuel. I am doing more troubleshooting tonight...will put up anything I find...oh also..not throwing any engine lights either.