I found a large document on bedding in new brakes to avoid the phenomonom that we incorrectly call disk warping. I have pasted an abridgment below and a link to the original text. Might be worth making this a sticky??
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The term "warped brake disc" has been in common use in motor racing for decades. When a driver reports a vibration under hard braking, inexperienced crews, after checking for (and not finding) cracks often attribute the vibration to "warped discs". They then measure the disc thickness in various places, find significant variation and the diagnosis is cast in stone.
When disc brakes for high performance cars arrived on the scene we began to hear of "warped brake discs" on road going cars, with the same analyses and diagnoses. Typically, the discs are resurfaced to cure the problem and, equally typically, after a relatively short time the roughness or vibration comes back. Brake roughness has caused a significant number of cars to be bought back by their manufacturers under the "lemon laws". This has been going on for decades now - and, like most things that we have cast in stone, the diagnoses are wrong.
In fact every case of "warped brake disc" that I have investigated, whether on a racing car or a street car, has turned out to be friction pad material transferred unevenly to the surface of the disc. This uneven deposition results in thickness variation (TV) or run-out due to hot spotting that occurred at elevated temperatures.
There is only one way to prevent this sort of thing - following proper break in procedures for both pad and disc and use the correct pad for your driving style and conditions. All high performance after market discs and pads should come with both installation and break in instructions. The procedures are very similar between manufacturers.
With respect to the pads, the bonding resins must be burned off relatively slowly to avoid both fade and uneven deposits.
The procedure is several stops of increasing severity with a brief cooling period between them.
After the last stop, the system should be allowed to cool to ambient temperature.
Typically, a series of ten increasingly hard stops from 60mph to 5 mph with normal acceleration in between should get the job done for a high performance street pad.
During pad or disc break-in, do not come to a complete stop, so plan where and when you do this procedure with care and concern for yourself and the safety of others.
If you come to a complete stop before the break-in process is completed there is the chance for non-uniform pad material transfer or pad imprinting to take place and the results will be what the whole process is trying to avoid. Game over.
In terms of stop severity, an ABS active stop would typically be around 0.9 G’s and above, depending on the vehicle. What you want to do is stop at a rate around 0.7 to 0.9 G's.
That is a deceleration rate near but below lock up or ABS intervention. You should begin to smell pads at the 5th to 7th stop and the smell should diminish before the last stop.
A powdery gray area will become visible on the edge of the pad (actually the edge of the friction material in contact with the disc - not the backing plate) where the paint and resins of the pad are burning off. When the gray area on the edges of the pads are about 1/8" deep, the pad is bedded.