1. Every FET has a body diode associated with it. When all the switches are switched off, the current is maintained in the inductor. This current actually "recirculates" (go read up on this term) through the body diodes from gnd to vdd. For this to happen, one end of the terminal must be one diode drop below gnd, and the other one diode above vdd, giving you a large spike (~vdd + 1.4V) across the motor.
2. Vmotor = Vbemf + Imotor * Rmotor + Lmotor * dImotor/dt
Various schemes for bemf measurement include waiting for Imotor to drop to zero, or maintaining constant current, and measuring the current whilst Rmotor must be known as such. Others play around with the math by introducing a series sense resistor whilst forcing a constant current, and cancelling the 2nd/3rd term.