Than the issue is definitely connected with rotors based from my experience. As for brake pads, I had vibration only with with cool carbon pads (two times with two sets, compound were overheating). I have tried many different manufacturers, such as ferodo 2500-3000, pagid rs19, hawk hps and hp+, porterfield r4s, ate ceramics and had zero issues. On my local bmw forum, people with e60 had similar problems with Zimmermann rotors. Good luck fixing it.
Off topic, I am planning to order front and rear f30 perf brakes in august and try to make them work in september. Thinking of creating interesting post with lots of description...