Awesome project. I don't think you'd be totally off starting off with the Q2's. I just used a Q2 rear at the Barber trackday on the new 10R, and I think it'd be great for a 600. I could see it either way.
In the old RRW write-up, they started off with a stock CBR1000RR as someone said, but had to replace the exhaust b/c of a rule against catalytic converters (or something like that). They also ended up replacing the rear shock (with Ohlins, I think) to give Toye more consistency as it heated up, and I believe they just tweaked the forks but kept them stock. Again, he put it on the AMA grid!
Super Streetbike did a write-up once where they put a stock bike on a track with a decently fast rider, took laptimes. Upgraded a single part, took more laptimes. They repeated the process with tires, exhaust, suspension, and I'm not sure what else, but it was a really good read to show what parts make the biggest difference.
Also, Taylor sounds like a good man for the job - he goes really well to be on a stock bike!! Also, he's had a lot of seat time on it, so it would take away the "new-ness" factor. Definitely keep us posted as this progresses!!!