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.
 
Good luck, it is pricey, but my only problem is a few inop gauges and I want long tubes but of course that's another story lol....my recommendation from a person that has the setup is to just cam out 04' DOHC setup and enjoy life. and mod your way in to the future, if you go 3V yeah you will be one of a kind but well not 1 becuase I have the setup too but it's a pain in the ass and takes years or that's what it feels like anyways, even searching for parts you always have to remember whether or not your looking for 97-04 part or a 05-09 part smh but overall if its what you really want do what you want with your money, my personal recommendation from experience would be a DOHC setup and retain all your electronics. Keep it simple and effective.