Setting ATmega32U4 timers

I've been searching for a couple days and I am not seeing how to set the ATmega32U4 timers (Arduino Micro). I need to run all 7 PWM outputs at the same frequency. I've looked at the Programming Leonardo PWM thread and a few timer libraries for other processors but it's not making sense how to adjust ATmega32U4 timers.

I know adjusting timer 0 causes delay(), milli() issues but the application calls for a very simple non-blocking PWM control loop for driving a gazillion LEDs based on A0, A1, and A2 inputs.

Out of the box, PWM pins 5, 6, 9, 10, and 13 are all the same (2 ms). Pins 3 and 11 are half that at 1 ms (timer 0B for pin 3 and timer 0A or 1C for pin 11).

I'll eventually figure it out after deciphering the datasheet but thought I'd ask here first.

Pins 3 and 5 in the plot both set at 95% duty