The rotor thing plagued me for about a year before I got mine sorted out. Went through all kinds of iterations on brake setup changes and kept having problems. There's no one answer to keep it from recurring regularly, but I can offer a mixed bag of various things that help:
1) Obviously, quality rotors. If the rotors genuinely have bad runout from the factory, there's not much that's gonna stop it from getting worse from pad deposits and heat. Of all the random brands and types I've tried on this car, the ones that held up the best were DBA-brand 1-piece and whatever 2-piece it is that Stillen's including in their APRacing BBK (not sure whose rotors they are really). You can check runout at initial install with a dial gauge mounted firmly relative to the spindle. Sometimes if the runout is minor, it can be corrected by remounting the rotor at a different hole offset to let the small rotor/hub variances level each other out (sort of like what a good tire place does with tires and wheels). There are only 5 positions to try, so just iterate until you get minimum runout on the dial gauge.
2) Pads! Often "rotor" problems are really pad deposit problems. Some pads are better or worse under different driving conditions about leaving patchy deposits on the rotor. Once any uneven deposit layer has built up, it tends to self-reinforce the pattern and make itself worse over time (like the ripples that develop in a dirt/gravel driveway self-reinforce from the suspension bounce of cars driving over them). Some of this isn't so much about a pad being universally "bad", just not suited to conditions (cold street driving vs hot race driving, etc). Using a very race-only pad on your car while you DD it between events can lead to problems. So can tracking street pads (although they generally just burn off anyways...).
3) Pad Bedding! Google about it, read ten different versions of the instructions for bedding different pads. They're all shooting for the same goal, and it's tricky, but if you read enough versions of the process you get a feel for what's really going on. Drive the pads with minimal braking for a while first just to let them seat level and wear into the right shape first (this is often left out of instructions it seems). Don't over-cook things on the break-in, and take extra care with the cool-down period after bedding. Try to time it out so you can get on a highway for half an hour at that point, in no traffic.
4) Stopping/Parking habits: don't ever bring the car to a halt on the brakes and stand on them. Ever. But especially any time the system's hot. That just bakes pad material into one spot on the rotor. Try to bring the car down to a very slow roll, then get off the brakes and let the car roll to a stop for the last few feet, especially parking or if you're going to be stuck at a light. It's hard in traffic, so just don't drive in commuter traffic if you can help it.
5) Driving habits, esp on-track: try to make your braking zones shorter and harder. You may get from 120->80 both ways, but doing it more abruptly (without locking the wheels, of course) generates less heat than dragging out the braking zone over a longer stretch. Less overheating -> more life. Try not to brake hard when the car isn't going straight, that puts odd sideways stress on things too. Trail-braking is fine, but that's different than slamming on the brakes too late when you've already turned in, which there's a hundred other reasons not to do.
6) Front ducts help a ton with not overheating the front rotors on this car.
And I know they're expensive, but the single best thing I've done for my brake situation is switching to Carbon-Lorraine's pads. They're not finicky about break-in procedure (they really don't even have a break-in procedure), and seem to maintain themselves and the rotors really well even under varying conditions (although they're still not ideal for a ton of street driving). They'll clean off deposits from street pads if you want to switch back and forth, too. The only real downside is the cost, but IMHO it costs less than throwing out barely-used rotors on a regular basis and having frustrating track weekends.
I'm using the CL pads now on the Stillen/APRacing BBK and I love this setup (+ Stillen's ducts + RBF600). I also tried the CL pads on the stock calipers (+ Stillens ducts + RBF600) with DBA 4000-series one-piece rotors and that went really well, too.
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