I understand the advantages of using the stock ECU (and Carey and company are way more experienced with all of this than I am) - but in situations like this, I wonder if a standalone ECU like MegaSquirt or Speeduino wouldn't be worth looking at.
I understand that the variable cams are the secret sauce, and I've got no idea if the rudimentary ECUs could handle it, but the whole "immobilizer" circuitry thing is really putting a brake on running a lot of tasty modern engines in alternate applications.