First off:

2002 accord 2.3L vtec

A little background: I bought this car from an auction a few months ago. It had a bad transmission (of course), so it sat a while. Since I didn't need it running right away, I did a ton of work to it in my spare time.
Repairs include:

-the transmission
-timing belt and water pump
-full ignition tune up
-complete cooling system overhaul
-throttle body cleaning
-drive belts
-cleaned maf sensor
-replaced o2 sensors
-replaced air intake temp sensor
-ran fuel system cleaner through system

Keep in mind, all parts used were quality parts. most were oem parts, especially the ignition parts. I also am unsure if it happened before the repairs, because I didn't drive it then.

Now, to the problem. The car runs perfectly fine. No issues outside of hot idling. When it's cold, it idles fine. Once it gets to or close to operating temp, it starts spiratically missfiring. There's no rythm to the missfires. Sometimes they're quite spaced out. Other times they're close together. I'm thinking it's something in the intake manifold gummed up, but I can't be sure until I clean it. Looking for ideas.


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WUT?
There is no MAF on the 90-02 cars. What did you clean?
Recheck your ignition system.
Verify the spark plug tubes are not leaking any oil.
Verify the spark plugs have not loosened or backed out.
Verify you have di-electric grease on the spark plug boots.
Verify the spark plug boots are not popping off. Use either Honda wires or NGK wires. Most other brands do not have the correct moulding for the boots and they pop off the plugs.
When you did the timing belt replacement, did you also verify the valve train was adjusted within spec? Too tight and the valves will hang open when the engine is hot.
Verify there are no codes stored in the PCM.
Verify the engine mount bonding jumper and all grounds and ground connections are clean and tight.
Verify the main battery leads are clean and tight to the battery.
Verify the battery is holding a proper charge.
Verify fuel pressure is within spec.