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Hi pantherairsoft,
I'm pretty sure the noise you are hearing in your setup is mostly due to the OC-2 creating sub-harmonics below what the pitchfactor was designed to deal with.
For example: the fundamental frequnency of the low-E is 41.2 Hz, and a partial 1 oct. below that is at 20.6 Hz, right on the edge of human hearing. 2 oct. below is 10.3 Hz, and most speakers don't even reproduce this, and it really just becomes extra noise for the PF to deal with when has to make pitch-shifting decisions in real time.
The bass mode setting in PF lowers the minimum pitch that the PF will shift accurately for, at the slight expense of tracking speed (but the lower pitch setting also buys you more polyphony). I would suggest using the bass mode, but I know for a fact that the minimum pitch in bass mode is set to a B0. (the lowest string on a 5-string bass). Any pitches below that might not always shift with musical results.
Also, it might not be what you want to do, but have you tried reversing the order, as in go from PF to OC-2?
-Russ