Alternator:
It certainly sounds like a bad alternator, but it would be worthwhile to first be sure the battery water level is OK. Most alternators are three phase AC generators with a full-wave rectifier for each phase, 6 diodes in all. When diodes fail, charging capacity is lost, 16% for 1 bad diode, 33% for 2, etc. A tech with an oscilloscope can quickly see if all 6 charging phases are present at the alternator output.

Brakes:
Coincidence aside (which is a possibility), the only thing I can imagine could have happened is some adhesion of a wheel to a rotor. So, as a consequence of removing the wheel & tire, the rotor was shifted, pushing the pads apart at that wheel. This should have self-corrected as the first application of brakes, but a shoe could be cocked or binding in the caliper guides (I've had this happen on other cars), resulting in increased piston travel. Does the car stop nice and straight if you remove your hands from the steering wheel (preferably in an empty parking lot)? Does pumping the brakes shift the brake engagement point higher?