When I go for the 1k check, my dealer will add the fork gaiters, a XSR900 handlebar and motor protections.
Then, if I find good deals I will take care of headlamp (XSR900 cup), blinkers and front fender. And maybe relocate the gauge.
I'll take care of the rear end later.
I'd like very much to modify the air intake but wont as long as the bike is under warranty.