Starting with the stock map should be okay provided:
- you change the injector parameters (scalar and latency) for the new injectors
- you adjust the CL--> OL delays to reduce the time of this transition (if they're anything like the extremely long USDM CL to OL delays)
If you do that, then there's enough margin in the stock ROM to use it as a starting point.
If you aren't self-tuning, I'd suggest getting a wideband and in contact with an e-tuner.