Jesse,
#1 like Jetboatguru says check your grounds! Is the battery the same as the engine block the same as the MSD box? Are the ground straps/wires big enough? And not corroded?
#2 Both of the big 'ol red & black wires MUST have a good/solid connections to the battery. I don't hink they have to be connected directly to it. (I like a power cut off switch between the battery and everything else.) But none of this, "Well there's power here, this should work.." Stuff. You need conenctins that can reliably handle quite a bit of current. The MSD works by converting a Ton of low voltage current to high voltage spikes. If its not getting a good current flow, it can't fill its capaciter. So your going to loose sparks.
When you ran the engine did it sit solid on one RPM? Like its being limied there? Or does it vary around some?
One thing you can do, for kicks and grins, is to take an "accurate" Volt meter, pull out whatever you have in the rev-limiter plugin, turn on the power and measure the voltage on both pins to ground. I one pin should be ground, and the other should be around 7 volts. That is, a correclty running 6AL is about 7 volts. If it is stuck at 3,000 RPM that would put it at.. {rustling of papers..} about 0.8 volts.
If you got this far, what do you read on the pins?
Hope this helps..
-jim lee