Rotors don't warp, what happens is the pad material deposited on the surface of the rotor is uneven. Usually happens if you get the brakes very hot, and then keep the brake pedal pressed, or park it, resulting in uneven cooling. See the article I linked.

Read this link

If you put the anti-squeal paste all over the pads, is there a chance any could have gotten on the rotor surface? Best just to use the high temperature grease on the the pad ears, where they touch the caliper.

Also, shaking can commonly be set off by braking, but not actually be caused by the brakes themselves. It can be any link in the steering, or suspension bushing, that can allow movement under a specific braking load. Since you had the vehicle jacked up to do the brakes, it may just be that the suspension pieces took a day to settle back into the position they were in before the brake job. Lots of locations could cause it in the steering linkage, thrust bushings, etc. Be careful of web diagnosis, as nothing replaces a trained mechanic actually investigating and looking for the root cause.

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