Hi,
I have also endured some strange going ons with my Rocket which sound very similar to your issue. I replaced. plugs, leads, TPS, half a wiring harness and tinkered with everything else without total success. No codes not a single fault anywhere.
(Crank angle sensor can also get cranky when they get metal shavings on them)
Once I was convinced I had done everything I could, there was nothing left to do but replace the ECU. Issue solved.
Fault: Rockets dont have external ignitors for the coils like many other brands. This signal tells the coil when the fire the plug. In my case I kept loosing a cylinder and when I had all 3 the bike ran pretty much as you describe.
If you have access to another ECU, I would drop that in first before getting into the black art of voltage & Ohms on ignition circuits. You will know immediately of the outcome thats for sure.
Mike