PC driven PWM for 96 Channel Motor Controller
You could consider the LT8500. It's a 48 channel pulse width modulator that can be cascaded easily to 96 - it takes its input from an SDI bus.



That gives you the opportunity to avoid bit-bashing with the more leisurely pace of SDI.

When it comes to the motors, you haven't said the spec but you will be looking undoubtedly for some form of H bridge circuit and there are quite a few in Linear Tech's portfolio and ditto Texas Instruments.

For SDI output from USB, maybe this would work and if not there are PCI to SD output devices: -