The engine does have an alternator, perhaps not in the familiar form we are used to seeing on autos or stern drive engines, the three yellow leads coming from under the flywheel are the alternator windings.
The grey wire on the terminal board is the tachometer lead, I suppose that could be grounded somewhere causing a problem. If the ammeter output tests come up low, you could simply disconnect that grey lead from the terminal board, I am assuming you do not have a tachometer.
I can not speak about your aftermarket rectifier, only the OEM stuff. Let us know what you see on the ammeter test.