Gen 1 Busa Turbo Sand Rail Spark/Fuel Problem

Thank you for reading. This is my first post. I have a sand bullet turbo hayabusa sand rail. Gen 1, no gauge cluster (for codes). Power commander for fuel and spark. It started huffing black a bit from the tail pipe before the last dune trip. Then a piston lifted a ring land and scrambled the valves. I've replaced a rod, base gasket, pistons, turbo gapped rings, cylinder block, head gasket, head, cams, and shimmed the valves. Leak down only 3 percent in worst cylinder. Cams not a tooth off verified many times. When cranking with coil packs off but plugs in, no problem. As soon as coil packs are installed, it gets very angry. Clanging during cranking can be heard and felt in frame. It will start and idle with some throttle input to start. Then it sounds like it's running on 2. It then starts rolling coal like a diesel truck. I then swapped the cam position sensor. Then swapped the stator/crank position sensor. Adjusted the throttle position sensor. Then deleted the dynojet boxes to bare stock ECU. Nothing helped. Seems like the blown top end was a symptom of the real unknown problem. I don't know what to do next. It ran great for years with the same exact setup. I've read many other posts but I'm coming up short. Please help!
 
Thank you for the reply. No offense taken. All thoughts are appreciated. Yes, from the sprocket chain side of the motor being #1 then 2-4 in order to the cam chain side. The coils are correct and verified two ways. the stock harness had little white tags that were numbered and we used the wiring diagram to recheck the colors of the wires and they all matched up.
 
Unfortunately not, there is no dash wiring. There is a port by the ECU a few inches into the harness. I assume that's for reading codes. I found a local dealer that was willing to scan it and tell we what they find. I plan to do that next week if nothing else becomes obvious.
 
Yes, I agree its an ignition timing and fuel timing problem. Either a bad sensor or bad ECU. Does anyone have a spare Gen 1 ECU I can swap to see if the ECU is the problem? Are there any Busa experts in the Vegas area, private or commercial? Thanks again for all your help and thoughts. Its much appreciated.
 
@sixpack577 is there a way to pull codes from the ECU without a dash?

Not that I am aware of, at least in Ecu Editor.
I do know that a gen2(I know the op has a gen1)will run normally Without the gages connected. I do not know of anything in the gen1 that would prevent it from also running normally without the gages connected.
 
Thanks @POWERHOUSE , I just found his number online and left a message. Im looking forward to his call back. I have been reading his Land Speed Racing articles too. Looks like he used to be based in Vegas.
 
I pulled the engine number from the back of the case. W701-143082. Does any one know how to find out what year that is? I need to make sure it's not a 99 or 00 without the restrictions in case I need to install a new ecu.
 
For the ecu
99 and 2000 are the same.
01 is different from all years
02-07 are the same.
Not including a few other supporting parts.
You have to change a few things beside just the ecu.
02-07 is ideal because they can be flashed.
 
I'm not sure how accurate the info is, but from THIS site it's a 99/00. W701- The W is 1200-1299 cc, the 7 is a 4 stroke 4 cylinder and the 01 is the first generation of the motor.
 
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