I have heard that in Honda's putting in a higher amp alternator with cause problems with the ECU. I was specifically told this when I mentioned retaining the stock alternator and having it rewound, anyone heard anything about this?
I have a Mazda 3 which has the same issues apparently. From what I've heard it's blown out of proportion though. As far as I can tell, the ECU only measures the voltage, not the current flowing through it, so unless your HO alternator also increases your charging voltage you should be fine.
Either way I bought a HO alternator myself. Haven't got it yet though.
Yes, a Honda ECU will monitor the current through ignition loads and turn off the alternator to save fuel when load is low (i.e. fans off). if you have a volt meter visible, you'll notice during both in town and highway driving, the alt is turned off when the Electronic Load Detector (ELD) has little current. The ECU sends 5VDC to the ELD and monitors the return voltage. As current increases, the ELD reduces that 5V. around 2.1VDC or below the ECU will keep the alt on. Above that and it will turn the alt off.
you're in luck. detail on the Honda ELD and my bypass are located here: