I was wondering what part I would need to make the signal automatically flicker back and forth between two separate paths. I am a rookie at this so any help/browbeating would be great.
i can think of a couple ways to do it, neither of which are very good

you would basicly need to create a timer circuit (there are clock ICs that would work) and then use the signal to control a "gate." i know ive actually done something fairly similar, but cant for the life of me remember the last segment of the circuit.

for the first half you would run your clock signal, and use one direct. the other you could invert (i would use an op amp running as a comparator) and use that as your second control. split your input signal into two paths, and use the control signal to turn one on and off, and the inverted to turn the other on and off. not overly difficult, but not your simple, everyday fuzz pedal build.

basicly sounds like you want a square wave stereo tremolo, unless i am mistaken. see what you can find for tremolo circuits and go from there.