I brought it to the dealer this morning. They guy at the counter, who is not a tech tried to sell me maintenance package that included synching the carburetors for $750. I politely reminded him it was fuel injected. Ugh. They said they would get to it in 2.5 weeks.
So to answer your questions CHawk, and thanks for taking the time to think about this.
You said that you replaced the ECU, replaced the wiring harness, swapped injectors, swapped coils, replaced plugs, and checked compression. Is that correct? Yes
The problem is in number 2 cylinder. Are you absolutely and unequivocally sure you are getting spark on that cylinder? You never described how you came to that conclusion. How are you sure of that? I put a little gasoline in the spark plug hole and it runs normal for a few seconds. Also, I put 3 different new plugs in that cylinder. Same result.
You said that when you initially pulled the # 2 plug it was black and sooty. That indicates to me that it was firing previously, indicating a failing plug, coil, or injector. When you run the motor now, is that new plug totally dry? Yes it is and there is no odor of fuel. I also swapped coils, and injectors.
When you swapped injectors, are you sure that the O rings on each end are installed correctly and that there is no blockage? (The fuel rail itself is not likely the problem since # 1 and # 3 are firing correctly.) Yes, I actually swapped them twice to be sure.
(This is the really screwy part for me.) Are you still getting 13.66 volts at the injector, and 12.4 volts at the #2 injector pin on the ECU? Test this again, making sure that the injector lead is not going through the harness clip. I'm not sure I understand this one. I replaced both the wiring harness and ECU so it should have solve any grounding issues. I know that I got exactly 12.0 volts when measuring the voltage at the plug that plugs into the injector itself on all cylinders, except the #2 cylinder, it read 13.66. Then when I measured it at the ECU pin it read 12.4. It is possible I got the wrong pin.
As Mike suggested, did you test the 2 P lead to the injector while cranking to see if you are getting a constant 12 V+ on the hot lead and a ground pulse on the negative lead? (You need an analog voltmeter for that.) I wasn't able to do the test while cranking.
Did you test the ground wire to the injector (the one that pulses to fire the injector) to make sure it is not grounded when the key switch is on?
I think these last two would also be resolved by a new wiring harness and ECU. I wasn't able to do the test because I have a digital voltmeter.
The guy at the dealer said the ECU needs to be paired up with the motor using the Honda software Is that true? The motor runs identically with either ECU.