Kiwi:
That is a really nice looking bike. It looks to be the definition of purpose built.
All:
Part of the reason I chose a 2005 R6 is that Yamaha made bikes with essentially the same parts from 2003-2009. It's also the last 600cc motor they made that was not drive by wire. I figured with 7 years of production and the attrition rate of "beginner" sportbikes would make for relatively cheap and abundant parts bikes. Today I went to investigate a craigslist ad for a reasonably priced 2004, and ended up bringing home 2 more bikes!! One is titled and driving, and one is in pieces but relatively complete. I've been having good luck selling parts on a certain auction site, and should at least make my money back on these 2 new ones while keeping 2 more motors and at least one extra set of wheels.
Bike purchased last fall:

Whole bike purchased today:

Extra frame and engine from today:

I now have a 2004 fork set (conventional telescopic fork)
(2) 2005 fork sets (inverted or upside down forks)
and a 2006 fork set (inverted and about 15mm shorter than the 2005 forks)
It seems to me that the conventional forks will be the easiest to lower in the trees because the diameter of the tubes on the inverted forks tapers and there is a very limited amount the forks can be slid up into the clamps. I've looked into shortening the travel for both kinds of forks (which I can do), and found (Thanks to this forum) a company that can shorten the entire assembly. I'm still a little up in the air about which front end to actually use. My thinking so far is that I want to maintain the stock distance between the top and bottom clamps regardless to maintain rigidity and that the inverted forks will give me a more solid platform to go fast on. If anyone wants to shoot some guidance my way on the subject I'm all ears.
In actual news, I do have forged rods on the way, started on my turbo manifold, and built the bed for my frame jig this week. Once the frame jig is closer to done I plan to start an actual build diary in the appropriate section here. I think I have the big picture figured out for the project and look forward to getting into the nitty gritty aspect of actually building parts and solving non-hypothetical problems.
Thanks for listening again...
~Scott