it sound like your fan control unit is going out. I am not aware of a method to check the fan control other than what you have already done. maybe HondaMechanic will chim in and give us his thoughs if a test procedure is available.
Test procedure to test wires to fan control.
Disconnect two connectors from control and check for loose pins, corrosion or damaged wires.
Test 1 Meter on Rx1000 between blue wire and ground 9500-10,500ohms.
Test 2 Meter on Rx1 between sky blue wire and ground should show continuity.
Test 3 Meter on Rx1 between green wire and ground should show continuity.
Test 4 Voltmeter between white/black and ground should read 13.0-13.2 volts (battery voltage) with ignition on.
Repeat with blue/red and ground and pink and ground. Should read 13.0-13.2 v each time.
If all wires test correctly, replace the cooling fan control unit.
the sky blue wire is the one in the 4 wire connector.
Got this procedure from Clymer service manual. Hope it helps.