I've haven't read the whole thread.. here's my $0.02.
to your last post, tires are the MOST important part of your setup. Then comes gearing, springs, geometry and damping. A perfect swing arm angle will do squat for you if the rear is spinning, old, sliding, under/over pressure. If you start chasing all sorts of setup stuff on crap tires, you'll be chasing issues that might go away with new (or even newer) tires.
to Lee's post, geometry can be a personal preference thing, most guys find that GSXRs do best on the track with more trail, so the front is generally raised (forks lower in the trees).
when my 08 gsxr 600 was running stock suspension, I liked it best with the fork caps flush with the top of the upper triple clamp and 6mm of shim on the shock. Rode GREAT!
I highly recommend you don't worry so much about getting the exact perfect geometry setup. A good baseline (flush forks / +2-4mm on shock) is a great place to start for an 06+ GSXR 600/750. Damping settings will vary depending on your pace, a good suspension guy at the track can help you get that near the target. Again, its your preference and area in which the bike will work just fine is quite large. The only way you'll learn how each change effects things is to try it out, BUT, for now since you're just getting started, just use a good baseline or whatever you're already comfortable and ride the damn thing all season.... Don't touch the geometry unless you have a problem that you know will be fixed by geometry changes.
Also, bikes have a wide range of settings that will work. Don't worry about having it exactly right.
Rob Sobottka is good with setup. He helped me diagnose a problem with old bike that was plaguing me for months!