polyglot:
One more thing: 1N4004 are really really slow (reverse-recovery time) and thus not suitable for use as catch diodes. You need faster diodes, e.g. a Schottky of some sort. Using slow diodes while PWMing the motor current can put high-voltage spikes back into your DC bus, and can also blow up the FETs by exceeding their Vdsmax (V = L * dI/dt).
Free wheel diodes only have to switch on fast to limit voltage rise,
reverse recovery time isn't relevant surely?
Or are you talking about switching losses with fast PWM as in a DC-DC converter. Motor PWM
frequencies are less demanding I think.