Yes, reversed polarity will make it run rough. it takes about 20% more voltage to fire the spark plugs from the "cold" side(the ground electrode) and most 6V systems don't have a lot of spark voltage to spare. Just change the battery cables around, and re-polarize the generator by touching a short jumper wire from the Bat. terminal of the regulator to the Arm. terminal for about 1/2 second. You'll get a moderate flash- - - -that's normal, not a short circuit. Crank up and drive on!
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
Cringe and wail in fear, Eloi- - - - -we Morlocks are on the hunt!
There is nothing noble in being superior to your fellow man; true nobility is being superior to your former self. - Ernest Hemingway
Love your enemies and drive 'em nuts!