Using an NB1 MS3 with a VVT motor?
 

I have a Brain-built MS3 that is currently set-up for my 99 motor, which is old and tired and needs a rebuild. I know of a pretty good deal on a fresh BP6D motor, but I don't know what I need to do to my MS3 to run the VVT in the new motor. I assume that I will have to add wiring that is not present in the NB1 harness. Is that it? Do I have all the hardware in the MS3 that I need to run VVT?

Ms3 has the logic already to run vvt. You need to find your wire coming from the ecu that says vvt, and wire that with a 12v power to the vvt solenoid and then change some settings in your ecu on tunerstuduo under the vvt tab. Then when your wiring is spot on you need to set your minimum and maximum vvt angles through tuner studio

I believe you need it to be a MS3X. The expansion card has the VVT capability. I may be wrong here since I'm going off of memory and I'm old.

If you have the expansion card then you need to jumper it to a connector close by to feed 12v and control to the VVT solenoid. An evap connector should do just find for this.

But either way you should contact Brain as he keeps documentation of the units he builds. Or so I seem to recall. I'm sure he'll lead you in the right direction.