Disconnecting the battery while it's running isn't a good way to check the alternator. It's OK for a '68 Chevy, but anything with computers isn't gonna like the voltage spikes that are created when you disconnect. Most of the time it won't damage anything, but once in awhile it'll fry your ECU.

Honda has an interesting feature to their charging systems. There's a signal from the ECU to the alternator, which can shut off the alternator. If the battery voltage is good and there's not much electrical load (measured by the ELD), the ECU will bring this signal wire down to ground voltage. If that wire is pinched (shorted to ground), the alternator will think the ECU is telling it to shut off.

Does he have the correct ELD for that ECU? (ELD is built into the fusebox.)