Originally Posted by the dude of dudes

Polling on other pins works, but I need it to run on interupts to maintain excact timing.

This is strange. Did you invert the intedg bit? the transistor inverts the signal.
Seems like you're working with an ANALOG signal? if this is the case you should use a comparator. The comparator module of the PIC16F88 can generate interrupts, if you like.