I've done a few mods to my bike (read my sig for some, not all are listed as I ran out of room) and have posted dyno runs along the way, I don't have access to post them again (they're on my home PC), but you can find them on this forum.
Best mods in my opinion are shocks, wheels & tyres, PCV w/ pipe and air filter (don't worry about modding the box, no point), then ergonomics to get the bike to suit you (bars rearsets etc). I personally found little difference in the ECU flash. I had the bike dynotuned before the flash and again after, their was improvement, but not as much as I'd expected. A good tuner will get your bike running smooth and nice without an ECU flash, but it does release some grunt in the lower gears.
There are also comparison Dyno runs (same day, same dyno) from Blanchy and Ballmead if you want to have a look at them as well to compare different mods.
Welcome aboard.