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Will it have all the updates installed with it?
Unless it's fresh off the assembly line, I'd say that it wouldn't. Here's the PitchFactor Software Update page for the procedure and the updates.
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Will there be an update that will feature an harmonic minor scale?
It's included as of version 2.3.0[2]. (Current version: 3.0.0[19]).
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I plan to run it through my effects loop. Is this recommended?
Many here do. A quick search through the forum will give you an idea of what to expect.
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I also have a reverb, flanger, and phaser that I run through the effects loop. What is an optimal order?
I might go with the PitchFactor – phaser – flanger – reverb, but experiment with the order. "Conventional wisdom" usually dictates Dynamics – EQ – Drive – Modulation – Time Based effects in a series configuration.
Pitch detection devices work best toward the 'head of the line'. I have several pitch-shifting 'boxes on either side of my drive / distortion modules. The PitchFactor is after the Drive, and before Modulation and Time-Based effects.
Keep in mind that these are generalities; open to debate, preference, and desired effect. But there are underlying practicalities and variables to consider in any routing.
