Trey,
this sounds like a fun project. Have you decided if you are going to get the best maps for each with the same ignition and cam timing for an equal comparison, or are you just going to see which tuner gets the best at whatever timing works for him?
With regards to the area under the curve issue, I did a simulation for times in straights at Mosport with increased power lavels in different RPM bands, keeping area under the curve constant, and if you look at the thread I started at
www.honda-tech.com/zerothread?id=404896, you will see where in the power band (with stock gearing and non stock gearing) you are going to reduce your lap time the most, and I would think this would apply to most tracks. I would concentrate tuning efforts in that RPM range.
I am looking forward to the results. Should be fun.