I agree with you that getting the 6 volt system working first is the best approach. Likely you have a problem that will cause the same issue in a 12V system. And if you do a conversion before fixing this issue - you just have a lot more stuff to possible consider (ALL the 12V mods you made).
The disconnected terminal is a good place to start. I'd think the previous owner disconnected this due to a problem he couldn't solve. Likely there is a short in the system, which you see when you reconnect the wire and see the current drain.
I don't think a wrong regulator would cause this power drain (with ignition off). However a stuck relay in the regulator certainly could. Pull the cover from the regulator and make sure all the contacts are free, and not welded together. Disconnect the battery first and press the contact with your finger and make sure the relay contact can 'make and break' freely. Also look at the relay contact surfaces and see if they are reasonably clean.
If the relay contacts look OK, connect the disconnected wire, and POLARIZE the generator (short the regulator GEN to BAT terminals for a second or so). See if this corrects the problem.
If not, you neet a voltmeter to dig deeper. Disconnect either connection to the battery, set the meter to AMPS, and check the current drain with the ignition OFF. You should not have any current in this configuration.
If you DO see a current drain at this point, you have a short in the system you'll need to find.
Finding a short can take some time. A schematic of your car will be of immense help in the diagnosis. Potential culprits include lamp sockets, door lamp switches, cigarette lighter, etc. The schematic will show you where you can disconnect circuits one at a time to find where the problem disappears - thus where you should dig deeper to find the real problem.
A possible time (and brain) saver would be to 'shotgun' the trouble shooting. Look carefully at all connections, 'jiggle' wires while watching the current drain, and you might find the problem in short order without having to go the logical deduction/engineering route.
Take your time, be patient, and remember that careful diagnosis will not only solve the primary problem - but will reveal other problems waiting to happen. Cleaning up potential issues now will prevent gotchas tomorrow.
Keep us posted, and if you have ANY questions, about using a meter to read current for instance, please don't hesitate to ask for help. Lots of good folks here are glad to assist and share our knowledge.
Good Luck!
