Pads: Lots of options and opinions available! Most of the people I've been around have used different combinations of Pagid yellow and black, and more recently I've been hearing people mention PFC pads. I used to use Pagid orange, then went to yellow mainly for longer life, and currently due to an incorrectly filled order am running yellow rear / black front, which is a common combination and seem fine to me. Honestly, I am not good enough to feel much difference in the compounds' behavior. The wear rate difference is noticeable, though! Cost per lap, maybe less so.
Rotors: Personally I like slotted, and think that drilled should be avoided because they will crack. I would go with inexpensive (but anti-rust coated) rotors because they all last a long time (as long as they don't crack at the drilled holes!).
The GT-3 ducts are supposed to be good.
Wheel studs are a godsend for easy wheel swapping! Get HIGH QUALITY studs and nuts from Apex:
Apex Competition Systems - Auto Racing Parts and Equipment
Brake lines: I don't have a good source for this because my current set are OK though not quite right, but make sure to find a source for flexy lines that can be PROPERLY MOUNTED. The fittings on the end not only need to be the right thread, but ideally should have the necessary outside shape/size to fit the brake line mounting bracket. At both ends of each flexy line there is a fixed mounting point (on the car and on the upright) that has a hole of a certain size that the head of the fitting should slot into, held secure with a little clip. I suspect many cars that have had the flexy lines replaced or enough caliper r&r cycles may be missing these little clips -- several of mine must have disappeared onto the floor of some shop years ago.... The reality is that as long as you can secure the 4 outer ends to the caliper brackets, things won't vibrate, but it's best to have all 8 locations properly mounted.