I've noticed that I can set D9, D10, and D11 to around the timer 1 can be set to ~244Hz. However I need 4 ports that are between 200-1000Hz but I have been unable to figure out how to find the last one. I can't really touch timer 0 as they control millis etc.
The ATmega32U4 on the Leonardo has 4 timers, named Timer0, Timer1, Timer3 and Timer4. Timer0 would be used for
Timers 1 and 3 are 16-bit timers, and Timer4 is a 10 bit timer.
You can get a wide range of frequencies by changing the prescalers and other factors. A bit would depend on whether you want them to all have the same frequency (but maybe with different duty cycles) or different frequencies. Each timer has two "ports" associated with it, so you can have different outputs - up to a point - for each timer. A given timer can only be in one mode at a time, which limits a bit what its two output ports can be doing at one time.
You could get a more detailed answer if you clarified what the exact frequency you want is, what mode (eg. PWM, fast PWM or something else) and whether each output should be the same or different frequencies.
According to the Leonardo product page:
PWM: 3, 5, 6, 9, 10, 11, and 13. Provide 8-bit PWM output with the analogWrite() function.
So even if you lose two to Timer 0, you should have 5 outputs left (it looks like the "B" side of Timer 1 and Timer 4 share the same pin).
According to Arduino Leonardo, you have available for PWM configuration ports numbered 3, 5, 6, 9, 10, 11 and 13. The specifications presented there do not provide the range of the frequency available, but I would expect that if you are able to use 9, 10 and 11, one of the others would fall into place.