Honda Accord 1994 Rough Idle, often miss cylinder 2-3 changed the distributer, the coil, spark plug, spark wire cleaned the egr valve, pcv valve, vaccum I noticed the engine miss the cylinder 2 and 3

Engine miss could be leaking egr valve gasket.clogged fuel injectors.weak coil. low cylinder compression.

You may have an intake gasket leak involving these two cylinders. Over time the gaskets will tend to harden up and not seal properly. You can try spraying intake cleaner in the area and see if the miss clears up. I have also used soapy water and spray it in the area. Be sure that it is spray and not a stream or water, and make sure it has a lot of suds with minimal water.

Fast idle control may need adjustment along with the IAC, however I think it unlikely that this would the cause of misfire. You mention cleaning the EGR, did you clean the EGR passages in the inlet manifold too? On Hondas the exhaust from the EGR is fed into each inlet runner by individual passageways. Over the years these become blocked but not all at the same time. Those that become blocked first cause their respective cylinders to run lean whilst the remainder run richer. This imbalance in fuel mix between cylinders leads to misfire. Eventually all the passageways become blocked and the misfire disappears as all cylinders run without exhaust gas introduction. It was around 94 that Honda introduced an inlet manifold with an access panel on the inlet manifold specifically for the task of cleaning the EGR Passageways. The earlier manifold had metal plugs that had to be removed to permit access which then had to be replaced with new ones once the cleaning procedure was completed. When all passageways are clear this possible source of misfire will be cured.

If all else fails and u still have issues try replacing your timing chain.

Sounds like a dirty Throttle Body and dirty IAC (Idle Air Compensator) valve. Get some good Throttle Body cleaner remove the flexible hose at the Throttle Body spray it and wipe it very very clean an old tooth brush works good for getting in there.

Now remove the IAC from the side of the throttle body, careful with the gasket if you want to reuse it. Spray it down good inside moving the valve back and forth as you do let it soak for a few minutes and clean it again. Blow it out with some compressed air and reinstall it. Put some throttle body/injector cleaner in the fuel tank.

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A check on the spark plugs of the 2nd and 3rd cylinder must tell the story. If you see there is a dirty plug, oil soaked or badly burnt we need to check on the firing and fuel delivery.
First of all check for compression if there is oil smearing, it can be due to weak oil rings or compression rings or a faulty bore in case the engine has clocked a great deal.
Also check the valve settings before the firing - spark intensity of the 2nd and 3rd plugs are confiremed. Check the HT wires to the plugs as you have checked the remaining sections. I hope this must give an indication of the lurking fault.