Well I guess I'll just go ahead and throw in my two cents about what little I know. When I started this thread, I assumed that the first thing to be done was to get some decent tires. But after witnessing the transformation a new rear shock provides, I am starting to think that suspension might just be the very first thing you need to address.
My bike is currently as follows. Renthal UL's, 900rr exhaust conversion, Pilot Road 2ct's, and an Ohlins rear shock (complete with unicorns and faeries!, seriously.) PC3 and Motivation sliders too. I'm going to have to address the front forks next.