6V positive ground was the standard in the 1940's and well into the 1950's. That's for tractors, cars, trucks, everything... 12V negative ground is something fairly new.
A quick test to see if the generator is okay: Connect the F terminal on the generator to the tractor's frame. If the generator starts charging there is something wrong with the cutout/regulator or the wiring or the ground.
I have a test lead with alligator clips on both ends for this kind of troubleshooting, though last week I used a piece of smooth fence wire to perform the test on my Dad's tractor.