Measuring audio phase shift through a circuit with a PIC

[languer]

This is most excellent.

You may have already corrected this, but on the original code the analog inputs for the comparators are not enabled (ANSEL.6 and ANSEL.7). Minor thing, but shouldn't hurt to follow the datasheet.

I do agree with other suggestions, since the inputs are already digital there is not need to use the comparators. But to use the IOC (interrupt-on-change) you would most likely need to go for PORTA or PORTB (which have individual IOC bits for each input).

General suggestion for interrupt use: keep everything short; do only the absolute minimum inside the interrupt routine.

Even though the use of the HW USART (HSEROUT) is a plus, you should still try to do this outside the interrupt routine. Do the timer stuff inside the interrupt (i.e. clear and set timer, etc). Make a flag that tells you the interrupt "fired"; and in the main loop manipulate the data to be sent out (and send it out). I think the CCP module maybe a much better candidate for what you are doing (duh, except you would need a PIC with two CCP modules - never mind).