Did the Jardone RT-1 race, PCIII, 15/47 regear, Double Bubble and tire hugger, Lockhart Phillips Aluminim race pegs, custom dyno map, full synthetic oil, etc...

Any other simple mods that actually make a difference? Better spark plugs?

 

One thing that I did to my last bike that seemed to help acceleration and response was a timing advancer. I have a PCIII USB, that I believe can be connected to a module to adjust ignition. With the above mods, would a timing advancer make a difference, or wou;d it be a significant undertaking with little or no pay off?

 

Put money into the suspension, especially if this bike will ever be on a track, or better yet, go to a school at a local track. Rider improvement is one of the best things that you can spend your money on.

Suspension: Contact Ed at www.tracksideengineering.com A lot of guys talk highly of him. I am going to have him redo my rear shock and forks for my weight.

If you don't like those ideas there are always tons of mods.
frame sliders
520 conversion (this will make a big difference due to the weight lost, but it seems you already at least went with new sprockets so maybe you went 520 at that time)
steering damper
stainless steel brake lines - front only, no use to put them in the rear (I use Galfer)
better pads (I love the EBC-HH pads, big difference over stock)
rotors (I wouldn't change out the factory ones unless they are getting old, they are pretty good).