Thank you for the info, for snubbing why don't you just have fast diodes across each device? As long as the DC supply is well decoupled by metal film caps near the devices that should deal with your ringing. But it is very layout dependent.
The common core for your supplies shouldn't be a problem since the windings are isolated. But a spike in one supply will typically be coupled to all.
Soft start is to ramp voltage and frequency at the same time, at least for your drive. Because the motor is inductive to keep currents reasonable as you reduce frequency you should reduce voltage V = L*di/dt, as MrAI stated.
To reduce the amplitude you just reduce the maximum PWM on duty cycle as you mentioned.