I have the same issue. It's likely due to deposits the brake pad leaves on the rotor. When you come to a hard stop and keep your foot on the brake afterwards (like most of us do) some of the super heated pad adheres to that place on the rotor, leaving a deposit. These uneven deposits can cause shaking similar to rotor warp.
There's a chance that different pads would help, or you could do the Tundra Brake upgrade - heavier / larger rotors mean less heating and less deposits.
The cheap / easy solution is to trying and avoid leaving deposits in the first place and occasionally rebed the brakes. If you have to come to stop from high speed, try and ease off the brake at the end, or even put it in park once you're at a full stop, that will let your pads and rotors cool while not in contact, which means less deposits. To rebed, find an quiet road where you can get up to a good speed. Come to a hard stop (which will heat the deposits and smear them evenly around the rotor) but let off the brake at the last second before you stop moving. Then repeat a few times.