I much prefer to have all my 12v on neg ground and all my 6v on pos, just to avoid what you almost got into when there's any jumping to be done.
If it were my ranch, I'd do with the M what Hugh suggested, give a look to see if it really is set up for neg ground or the battery's just in backwards. If the latter is the case, it's fairly easy to turn the battery around. Before starting the tractor, repolarize your generator with just a quick touch of a jumper between the BAT and GEN terminals on your relay, run it and see how it charges. Can't rule out the relay or regulator having been cooked with the reversed polarity, but it may still be okay.
If it is truly set up for neg ground, that's still fairly easy to switch to pos if you want. Unhook your battery and swap the wires between the poles on the back of your ammeter. If you have a battery igntion (as opposed to a magneto), you'll need to swap the two small wires on top of the coild, so that the wire from the battery is connected to the - pole, and the wire to the distributor and points is hooked to the +. From there, you should be able to hook your battery back up, repolarize as described and go. There may be a hitch if you have a regulator that is designed for negative ground only, but try the rest and see what you get.
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