2v To 3v Swap With 3v Ecu

I am in the planning phases of swapping my 2V for a 3V. I have read tons of threads thus far, but all of the ones that I have reviewed account for using the 2V ECU and not the 3V. If I go through the hassle of doing this swap I would prefer to use the 3V electronics with the VVT. I know FRPP sells the Control Pack with the pedal assembly and ECU, but my question is what to do with the factory ECU/Harness? Do I remove all the engine associated wiring from the harness and replace with the 3V wiring and ECU or will I have to somehow run both? I know this will be a big project to take on but I think in the end it will be worth it. Any input is much appreciated, and much thanks to the guys who put in all the time on the 3V threads i have read so far. They have been a huge help in the initial phases but now i need to get this last part figured out.
 
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