Please update...I am interested in this problem as I have been tracking down the very same issues for over a year now. Cold or Hot engine, it would for no reason studder/loose all power/no acceleration, at 3K RPM. No throttle response at all, then for no reason again, it would come back on. Very "jerky" and I can only imagine what this is doing to the clutch and tranny.
I also have also replaced, like you have:
-Distributor cap (oem honda)
-Rotor arm (oem honda)
-Plugs (NGK laser iridium)
-Oil & filter
-Fuel filter
-TPS (oem quality, set up correctly for closed and WOT)
-MAP sensor (oem quality)
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IACV (oem honda)
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Spoon leads/plug wires
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Fuel pump (255lph)
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Coolant temp sensors (both on the head)
and still the issue remains, but with a twist, the issue has gone into hiding, it has cleared up for no apparent reason...because it stopped happening well after the last effort to fix it. I last changed both coolant sensors on the head: sensor going to the ECU/ECM and the sensor going to the dash. I was still having the issue after changing the sensors. But one week later, I no longer have the issue. It has gone into hiding...