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1. True up the faces. This is to wear away high points, mainly of the pads so that the pad and disk are in 100% contact. This is often the largest single cause for the brakes not feeling great as you can easily have as little as 10% of the braking surfaces in contact for the first few miles. This is easily checked as the new disks will be scored with shiney lines where the pad is making contact. This will grow over time until the whole pad area is in contact, but a 'bedding in' procedure will almost certainly cure this instantly.
2. Remove surface contamination from both pad and disk surfaces (oils/greases, zinc coatings on disks, glazed surfaces of new pads, rust etc).
3. Transfer of pad material to disk. This involves coating a layer of pad material on the disk surface at a molecular level, as there are 2 forms of friction generated during braking, with the 'pad - pad material' (on the disk) friction actually producing much more friction and therefore better braking effect than the 'pad - metal disk' friction. Again, the 'bedding in' procedure below deals with this.
Assuming you changed to ATE racing fluid or something silimar and flushed the system very well, then try a full bedding in procedure below and then see how they feel....
Bedding in - The best thing to do is to find a long, straight, empty road (such as a country road between 2 quiet villages). Now perform 10 acceleration and braking runs, where you gently accelerate to a around 80MPH (theoretically you should slowly increase from 60 - 80+MPH according to the car and brakes) and then brake increasingly hard down to 5MPH. Never trigger the ABS, just aim to be at 95% braking on the last few runs.
Also NEVER STOP as you will leave a pad imprint on the disk surface - this is a life rule, not just for bedding in sessions - never sit at the lights with your foot on the brakes, if you braked hard and the brakes are hot. The pad imprint will cause brake judder that is often misdiagnosed as warped disks. In truth, it is virtually impossible to warp a modern disk!
The reason for accelerating slowly is to allow the brakes to half cool before the next stop. This puts the disks through a beautiful step up heat cycle, slow climbing until reaching the highest temp on the last run. You should notice a brake pad smell after the 2nd or 3rd run, which should have gone by the 7th-8th run. This is because you will have reached a high enough operating temp to have burned off all the surface contaminations and since the pad should now be 100% flush and therefore in contact with the disk, you will have transferred the pad material to the disk.
When you finish, the disks should be hot and a very even (slightly blue) colour across the entire contact surface. If for some reason there is still a small area of lack of pad contact, you can do a few more runs.
Believe me, this is the best way to bed in brakes as normal driving for 100 miles will not heat cycle the disk enough and will not generate enough heat to get a good transfer of pad material to the disk. It may also just not be enough to align the braking surfaces, particularly if you are not confident in the feel.