Zed.........there are many ways to convert your frontmount 2N to 12 volts, some of 'em even work.
Sounds like the converter used the ol'hog'em out technique. This scheme gutted the frontmount ignition coil and basically threaded an externally mounted 12 volt coil sparkies thru the shell of the 2N's frontmount coil. And also snaked out the wire for the points.
This will work, but then when some unsuspecting, electrically challenged, new owner has problems, nobody can really help too much, because the new owner donna know from nuttin'. And then the pressure from the helpmate......gaugh!
I really don't think there is a direct relationship between discharged 12 volt battery and gutted ignition coil except twas done by the same knucklehead.
What would I do? I'd do some searching on 12 volt conversion on the internet and studdy how it was done. Once I had a basic understanding, I'd probably throw the present kluge innna trash and do a more conventional 12 volt conversion using the standard 6 volt frontmount ignition coil and the "infamous ballast resistor" mounted on the backside of the dash AND a 12 to 6 volt converting resistor. Connect the two aforementioned resistors in series (like flashlight batterys) from the ignition switch to the coil terminal. You should read about 3.5 volts (2.5 min, 4 max) with the points closed and battery volts with points open. Anyother volts gonna give ya sparkies problems.
Then ya gotta worry why the battery won't get charged. This could be anything from bad battery, bad alternator, bad wiring, DUMB conversion. I'd get both the alternator and the battery checked at the autoparts place and then figger out how to make certain the wiring was done per the scheme that I found searching the internet.
I love 12 volt conversions done correctly, and curse those that think they're smarter than the book. If'n you still don't know or understand whats going on after you've done some research, please ask for more assistance.........Dell