Just keeping that old regulator in the vehicle can lead to some confusion. It's completely superfluous if that's the proper term here. If you are going to retain a modern, internally regulated alternator, whether 1-wire or standard, you not only do NOT need the old regulator anywhere, any time, but should remove it just to avoid clutter and confusion.
The actual regulator that does the work is now inside the alternator and always will be.
The ammeter does not work, or will work only sporadically because it's literally no longer in the loop (literally). The ammeter is on the Black w/yellow wire still, but the Red wire for the higher output alternator literally is bypassing most of the current flow. The ammeter will mostly only show something from the fuse box that's using power now. But the battery is being charged for the most part, directly through the Red wire.
As you suspected, 12v while the engine is running is not enough. Should be 13.5 to 14.5 for a good reliable efficient charge.
The Green w/red wire is not needed on a 1-wire alternator. Only a standard internally regulated wire like a standard 3G or similar.
The Yellow wire is no longer in use either.
The Orange wire from the old regulator is obviously not used, because nothing from the old regulator is needed.
Not sure exactly what the short Red wire between the side terminal and the main terminal is doing on the alternator either. On 1-wire setups one of those terminals is for a dash charging light to let you know if the alternator is not working.
I don't want you to damage a good alternator, but since it doesn't work anyway, you might consider unplugging that wire and seeing what happens.
Better yet, contact or check the websites of several of the fancy alternator companies. I don't see any labels on it, but you might check underneath just in case. Could be a Tuff-Stuff setup, could be from one of the serpentine companies, or even MSD (though it does not look like an MSD unit to me) or any of a number of companies. Be nice if it had some identifying markings on it so you could find out just what that wire is doing there on the side.
Maybe that's in the Painless diagrams? Have you spoken to Eric yet by any chance? He's the Painless guy that made the harness and wrote the instruction book on it too. You can PM him through this site as well, via eric0o1 here.
Of course, you really should take the alternator down to a local auto store, if you have one with technically savvy employees, and have them test it.
Good luck.
Pauil
