Good point about making sure to test the device at a low current first. I will probably buy 10 and 100Ohm resistors and then test them at a lower amperage to see how much they decrease the PWM.
As for the ceramic decoupling, would putting some capacitors in parallel with the H-Bridge work for this?
I will definitely make sure to put resistors between the H-Bridge and board, and I will probably also use a relay to prevent shoot through from a programming error