Ha! Welcome to the forum Bigblock
Reading your laundry list of mods is like reading my receipts from the shop. I'm currently trapped, Rocketless, as they put the Triple K&Ns and PC5 on and powder coat my wheels. My Jardines are on order (should be another week or 2). I have a Corbin Fast Gun being built for me now, and a Chin Fairing on the way from Custom-Sculpt.com. If I don't self destruct from impatience first, I'll finally post some pics of my bike when I get it "finished" ('course then there's paint, maybe a slight riser kit, suspension upgrade, headlamps... mumble... mumble)
I haven't bought many fiddly bits yet, but I have the Triumph Heated Grip kit (New York gets brisk in the winter) and I'm planning to replace as many little plastic pieces as I can (brake line clip that never holds, control line guides, etc.)
Just a note, I don't think it'll hurt you to have the PC5 with Auto Tune, especially if you buy it first and do the rest of your mods in stages, but if you're planning to do all the work at once and Dyno anyway you might just be throwing away $300 on the AT unit.