mud racer truck missfire only when alt. is turned on?

my race truck has everything toggled.
including the altinator...
when its turned on there is a mild miss in the engine , as soon as you turn it off it goes away.
Any idea's???
13.6v at 2000rpm's

Do you still have the factory wiring from the alternator to the voltage regulator??
If so untape the wiring and check the soldered area where 4 or 5 wires are hooked together. The soldered connection gets corrosion and will cause lots of constant or intermittent missfiring and dieing troubles.

Hope you get it fixed
mike