dude, First things first, are you still running the std brakes or are you running the 260RS brembo's? You haven't said wether the car is stopping OK or not?
start from the end and work backwards.
: As duncan said, don't worry about the discs, they will scrub up OK once you have been driving for a while. Just pretend you are bedding in some hard pads and it will be fine. Just make sure they are not warped.
: Callipers - are you 100% sure you don't have any stuck pistons? Also have a good close look at the callipers slides. I always give these a quick touch up with some 1200 grit wet and dry, a really good clean, and a very light smear of the best high temp grease you can find at pad change time, but if the car has been sitting then any surface rust could be stopping the calliper from positioning the pads properly.
: Pads - It may be worth popping the pads out of the front and have a close look at them. Don't just look for wear, but also for the overall shape of the pad - Are they excessively tapered front to rear (of the car, not the pad)? This may be due to insufficient "knock off" from wrong braking methods, Also, look for shiny spots on the face of the pads - this could be a sign of hot spots (also due to insufficient knock off) All of these will lead to false readings from the abs
: Fluid - Never underestimate the ability of brake fluid to deteriorate. I would drain and flush the whole system one wheel at a time, paying close attention to any difference in pressure from wheel to wheel, if you have any crud built up in the flexible lines it may be restricting return pressure even if it stops OK, leading to some pretty confusing readings for the ABS to figure out.
: Master Cylinder - Check all the obvious things such as vacuum to booster, signs of leakage from the master cylinder, etc etc.
I hope some of my ramblings help, but when all is said and done, it could just be the ecu change......