2007 Hayabusa missing 2 cylinders

I am new to the forum, so please forgive any mistakes. I have combed through the problems forums and haven't found anything quite like this.

I have a custom built C Sport Racer (SCCA designation) with a 2007 Hayabusa drivetrain, flatshifter, power commander III, and a custom header/exhaust (to fit it into the car application. I bought the car about four months ago and have not had it running perfectly yet. It sat for around a year without much use before I bought it. I changed the fluids, drained the fuel cell, cleaned out the fuel filter, cleaned the fuel injectors, and replaced the spark plugs (NGK CR9Es).

I took it to the local dragstrip the other day and it squeaked out a 13.5 at 110. Keep in mind the car is 1150 lbs dry. It was backfiring and way underpowered for the whole day other than that run. For whatever reason the stars seemed to align and give me at least a moment of fun.

Most recently I discovered that it seems to not be getting spark on the #1 and #4 cylinders (outermost cylinders on both sides). This makes sense because I had noticed that it seemed to be running rich (fuel in the exhaust when cold and backfiring when hot). I identified this by unplugging the coils one at a time while the engine was running and noticed that the engine showed no change when unplugging 1 & 4. To confirm, I also swapped around the spark plugs to confirm it was not them, and the issue stayed with 1 & 4. Then, I swapped around the coil packs, and the issue stayed with 1 & 4. I tested the resistance on all four coils and they came back equal (about 10.28 I think...). I tested that the coils are getting power (voltage test on the power wire to each coil pack) and that checks out as well. I have tested the Cam position sensor and the Crank position sensor and both have resistance in line with the manual. Just to be certain, I also pulled the injectors, cleaned them, and swapped them around as well. The problem still remained at 1 & 4.

Has anyone had or heard of a similar issue? Any advice or thoughts?
 
Did you by chance try turning the motor over and ground the plugs out on the motor to visually see the spark?

You could have bad plugs. You could take 1 and 4 plugs and coils and put them on 2 and 3. See if it follows.
 
Odd behavior like one bank not firing? => Grounds are good, ecu ground wire secure?

Are there other accessories (just checking in case you forgot when you wrote the above) like a timing retard eliminator that could be removed for troubleshooting?
 
Odd behavior like one bank not firing? => Grounds are good, ecu ground wire secure?

Are there other accessories (just checking in case you forgot when you wrote the above) like a timing retard eliminator that could be removed for troubleshooting?
I have verified all of the wiring, but will do so again. All the grounds that I have seen seem to be clean and secure, but will check them again. Are there any grounds that I should be aware of that come up as typical troublemakers? Keep in mind this engine and trans has been transplanted into a car and the build quality is pretty damn good.

there are no other mods or accessories that I know of. I tried running it without the PC III and it does the same thing.
 
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