Cant run a CDI box to work on my 1G

[GSXftw]

So Ive been running stock coil pack, good wires, I found the limits on that with water/meth and blowing spark out. The car runs fine otherwise. I bought a used Dynatek ARC2 made for a dsm with the install harness. When I put it on it will fire on all 4 cyl but will drop to 3 it seems, and it gets a DTC 0044, ignition circuit failure. I figured the box was bad, so I bought a brand new CDI box, SAME THING! Any ideas?
Power/ground wires are straight to the battery and are good, also Ive been trying to go to a COP setup, and it does the same thing, so can rule out the coil pack

 

[GSXftw]

Update, all cylinders have excellent spark, but 1/4 spark grounding out doesnt change engine RPM, so 1/4 are down while CDI box is hooked up, only thing I havent changed is the black box in the harness whatever that does

 

[97 eclenger]

how do your spark plugs look? I've had a few plugs with cracked ceramic so the spark was arcing with weaker spark. just a thought. or plug wires split open in section

 

[GSXftw]

how do your spark plugs look? I've had a few plugs with cracked ceramic so the spark was arcing with weaker spark. just a thought. or plug wires split open in section

Plugs are good, new engine, 900 miles, The spark is very strong on the CDI, jumps like an inch, it does this same thing on the COP, so rule out wires/coil

 

[tmoney20g]

I've heard the spark, with a CDI, can arc UNDER the boot, so if you're boot is too short, the spark could arc to the spark plug galley wall in the head. Maybe boots for 1/4 are cut too short ?

 

[GSXftw]

I've heard the spark, with a CDI, can arc UNDER the boot, so if you're boot is too short, the spark could arc to the spark plug galley wall in the head. Maybe boots for 1/4 are cut too short ?

Good thought, but it does this with good ol MSD magnecore wires also, and they wrap up the plug like a good pair of mittens

So the update on this is, the CDI box is causing injector pulse to cut out on 1/4. Why I still have no idea

 

[GSXftw]

Heres a log and an update.
The car only runs on 2/3 while the CDI is hooked up, It loses injector pulse on 1/4, injectors still have power just no pulse. I tried replacing igniter, injector resister, coil pack, I directly grounded pins 101/106 chassis ground on the ecu since I found a bit of voltage drop across there, directly grounded all ignition components (coil, igniter, ect) went to COP set up, visually checked ecu, looked good no leaky caps, still same thing. It doesnt run all that great without the CDI either, its starting to misfire on part throttle, breaks up at 15 psi or above, and occasionally will only run on these 2/3 cyl on start up then clear up and do all 4, so for this reason Im not suspecting the CDI stuff, more like the extra load from it is making my problem surface.
Come on people lets put our heads together we can find this! Race season is here in less than a month! Notice on the log the ridiculous amount of wideband action (misfire)
Also if I didnt mention this is a brand new engine, so new plugs, new wires (when Im on wires) this log is with the COP, which made it worse. I read I was supposed to see a 2-4v pulse at the igniter on wires yellow/red, and straight yellow, I only see .24 or so, could this be the issue? Im kinda stumped on what to troubleshoot at this point

 

[GSXftw]

Nothing huh? Come on peeps