Hi eeyore and although you have posted up a fair bit of info, still need a bit more.
From what you have posted, to get only 12.1v reading, if this is with the battery connected and it should be, then you probably have a problem with your battery.
Never run your motor and disconnect the battery, this can in a very short time period, stuff your alternator.
Now back to the voltage.
If your battery is in a low state and as you only have a 40 amp alternator, that low voltage could easily be caused by the battery pulling more current than the alternator is capable of producing.
In situations like this, and this is very commonplace, when an alternator’s maximum current production is exceeded, an alternators voltage drops. Again, this sort of situation is commonplace.
Again, if your battery is low, and as your alternator would be unlikely to produce as much as 15 amps at idle, it would be easy for your battery to try to pull way over 15 amps if it was in a low state.
Try leaving everything alone over night and before you do anything else to the vehicle in the morning, measure the battery’s voltage.


. OEM 40amp Nippon Denso alternator has been rebuilt by local auto electrician last week. Regulator is 6 months old, solid state, internal fuse good. Pulled dash apart (a mistake, since it was held together with self-tappers, silicone and hope) to check indicator light and found that it's wired differently to the manual's circuit diagram. The Batt/Alt indicator lamp isn't connected back to the regulator harness at all, and the wires that should form that circuit are connect together via a very heavy fuse. Weird, since I thought it wouldn't have ever worked without the indicator lamp in the regulator circuit? 
				
				
				
					
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. (And I was a bit hesitant about posting about this problem because of how much info seems required in order to diagnose electrical problems!)
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