On the E53, I've used ATE rotors, which rusted, and OE BMW rotors from the dealer, which came with a special coating and didn't rust at all.

The squeaking is the pad vibrating, and you will hear it if there is a transmission path for the vibration. That is what the plastic goop tries to do, when applied to the back of the pad. It isolates the pad. The problem is that it squeezes out over time, and the noise returns. The only product I use on pads is a special high temperature caliper grease, applied to the ears of the pads where they contact the calipers. Also, make sure the anti-rattle clip is tight.

BMW lists 30,000 miles (Inspection I) for cleaning the pad ears and reapplying caliper grease at that point only. Make sure that the grease doesn't get applied to the guide pins, which are designed to be dry.

Brakes can be done DIY, but they are also a safety system. It is easy to replace parts, but properly inspecting brakes for safe operation is more involved. If they are assembled wrong, you are likely to put it back the same way and not know how it should be assembled. If you haven't done a complete brake job before, do it with someone who does have proper training.

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2007 X3 3.0si, 6 MT, Premium, White

Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue