As for the PWM outputs, they use interrupts, and if I designate an interrupt for my own use I have to give up one of the PWM pin pairs, correct?
I'm not sure what you mean by this. The PWM outputs don't use interrupts. They can raise an interrupt if you want them to.
Do the external interrupts intefere with the ability to do PWM, in the same way that timer interrupts do ?
No interrupts interfere with PWM, that is generated by the hardware.