The advice I was given follows. I will try to remember it as best as I can. Keep in mind that unlike Jim, I have no EFI experience. He is your best contact. This is what I was told.
First, you need to find a bike shop with a dyno and an operator who knows about EFI mapping. Portland is a small city and the fellow could name at least three business that do this. This is not an uncommon thing to do.
Second, talk to the shop about the software they are most familiar with. Tune Edit, like Jim says, or Tune Boy, or Power Commander, or another that I cannot remember. Use the software they have the most success with.
Third, do your engine mods. Bring the bike in and let them install the chip, set it up, do mapping or whatever for your mods using their computer and dyno, and let them test everything.
This is like what we do with the carb bikes. The only difference is they swap jets for us instead of changing maps.