Issue with crane cams hi-6 cd ignition

I have been having a strange issue that I finally narrowed down to being ignition related some how.
At first I thought it was a drivetrain issue on my 91 w150 4x4 truck.
The issue I was having was a horrible vibration that came on at 2500 rpm.
I figured out the vibration showed up at 2500 rpm in every gear, and then realized it was showing up in nuetral and park as well.
I decided to hold the throttle at 2500 in nuetral and listen really close and I've determined it's a really bad miss fire.
It starts sputtering and popping out the exhaust, I checked my spark plugs and they are good, ohmed my plug wires, they check out, checked resistance on my ignition coil, it checks out.
I have noticed when I'm holding the throttle at 2500 rpm and it's in the middle of it's Miss firing fit the little red light on the crane ignition box is going in and out, getting brighter and then dimmer and brighter then dimmer.
And the box it's self gets awfully warm to the touch while this is happening.
I'm pretty confident whatever is causing the miss fire is inside that ignition box somewhere.
My first thoughts are, could the rev limiter be malfunctioning, glitching in and out at 2500 rpm?
Or could a bad ground to the ignition box cause something like this?
I'm wondering if there is anyone else that has encountered an issue like this with a cd ignition box, and if so what did you end up doing to fix it.
Distributor is a brand new firecore 50 with less then 100 miles run time on it, plug wires are Taylor thundervolt 8.2mm wires, coil is a crane cams lx91 e-core style coil.
Distributor cap and rotor are brand new.
Pick up coil checks out reisistance wise.
This is just really strange.