Controls Remove everything except the throttle, brake, clutch and kill switch. You can, if you wish, remove the choke assembly, but that makes for much harder starting. Mine still has it. As it weighs about 12 grams I'm not too bothered by this. The Bridgestone weighs less, and turns quicker, but wears out faster.
Brakes Throw away the standard hoses and use braided steel ones.
As far as pads go, it's up to you. Currently I'm using EBC HH, but SQS RQ and Ferodo CP901 are also very good. Some riders replace the standard disk with an EBC Pro-Lite, and I will probably go the same route when my standard disk is shot. There's very little scope for modification here. Run the rear pre-load as high as you can get away with to increase ground clearance, without chewing up the tyres.