Isolating PWM From H-Bridge
So my main question is, what is the best way to isolated timing
  critical signals?


For an application like this I'd consider sending only one PWM signal through one opto and, at the H-bridge side, recover that signal and apply the inversion and necessary timing differences to prevent shoot-through.

Here's a circuit that can avoid shoot thru by introducing a dead-band i.e. no overlap: -



Using a small time constant RC low pass filter and schmitt trigger OR and AND gates you can manufacture two PWM signals from one - all you should need to do is invert the output from the OR gate and you have dual, complementary PWM signals with shoot-thru protection.