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Since I got these pedals 6mos-1yr ago, I've had them setup in several different ways. I started using them all before the amp, and they all sounded good there, especially the TF, but the MF, too. I usually use the MF last because I like my echos to be modulated, instead of echoing my modulations, but that depends on what sound I'm trying to get at the moment.
I also tried running the PF in the loop with the TF >> MF in front of the amp. Got some great sounds that way, too, but some of the more dense echos sometimes confused the PF scale-tracking (understandably). My current configuration goes like this…
guitar >> (input) Boss NS-2 (send) >> Keeley Compressor >> Morley Bad Horsie >> (in) amp1 (loop send)
>> (return) NS-2 (out) >> (mono) PF (stereo) >> (stereo) TF (stereo) >> (stereo) MF (stereo)
>> (loop return) amp1 & (loop return) amp2
MIDI-wise, I've got TF >> PF >> MF. I'm using the TF as the MIDI CLK source, so it's first MIDI-wise, which is slightly backward from my audio chain.
Control-wise, I've got 3 Digitech FS-300 triple switches and 3 EB VPJr25ks with one of each plugged into each of the three factors. On the PF, the ext switches control tuner, flex/learn, and bank down. On the TF, they control repeat, tap, and bank down (or record, play, and stop in Looper mode). On the MF, they control tap, brake, and bank down. Mostly, I use the expression pedals to control modulation speed and depth (MF), delay time, mix, and feedback (TF), and pitch or mix (PF), but that really varies by preset and what I want it to do.
I know what you mean about the phasers not sounding quite right in the loop. It's like putting a compressor in the loop; it does what it's meant to do, but the end product is not quite what you expect as a guitarist. Somewhat strangely, the rotary effects in the MF seem to work better for me in the loop. So, I've ended up spending a lot of time playing around with the phaser settings trying to tame them down a bit. I ended up with passible versions of my Phase 90, Phase 45, Small Stone, and Ross Phaser. Maybe not exactly the same, but close enough that most casual listeners wouldn't notice. I'm still trying to find a better Univibe type sound, and I seem to be getting close, but it doesn't have enough of that 'thump/whump" when it reaches the bottom of the oscillation cycle. If I was recording something that needed a Univibe sounds, I'd probably dig out my DejaVibe, but it's passible in a live situation.
Also, I think the quality of the phase effect is noticibly better after the V3 update. I think the trick to getting the phase tamed is in the combination between the Intensity and Depth settings. I think there's still room for improvement on this one, and I'm still hoping for the addition of a Univibe-specific option.
While the following examples seem to be working for me, with my guitar, my amps, and my fingers, and at least for now, you might try some of the following… I use the expression pedal to switch between (slow) and (fast) and when playing, I almost always grab it instantly and tweak until I find what I'm looking for at that instant. So, some of the range of settings, as noted below, may be a little over or underwhelming unless you use values that are in the middle of the range of those settings.
Phaser: Intensity=45, Type=PhaseXO, Depth=75, Speed= 0.12 (slow) or 7.01 (fast), Shape=Triangle, Xnob=2 (slow) or 6 (fast), DMod=20, SMod=10, ModRate=0.50 (slow) or 0.25 (fast) (I intentionally inverted this setting), ModSource=Random, and Tempo=Off.
I've also had luck with the Vibrato… very phaser-like. Intensity=50, Type=Retro, Depth=50 (slow) or 25 (fast) (again, intentionally inverted), Speed=1.00 (slow) or 7.01 (fast), Shape=Sine, Xnob=24, DMod=10, SMod=5, ModRate=0.12, ModSource=Random, and Tempo=Off.
The Leslie is really good, too. Intensity=75, Type=Standard, Depth=0.70 (slow) or 6.92 (fast), Speed= .98 (slow) or 3.73 (fast), Shape=R99/H99, Xnob=45, DMod=36, SMod=36, ModRate=6.14, ModSource=Random, and Tempo=Off.
In any case, I'm still working on going through my old presets and tweaking them for V3. If you'd like, I can send some others to you once I finish with them either via post or once the new FactorLib is released.