Anyways! I promised a write-up on diode differences, so here it is! If you don't want the technical details, please scroll down, but I think this may help you understand how they interact better.
The basic difference between diodes in a clipping circuit is their forward voltage-- that is, the voltage at which they conduct. Basically, when the voltage (volume/gain) of the signal gets above that voltage, the diode will conduct-- usually directly to ground or to a "virtual ground", either way the effect is the same-- the signal clips. So, if the forward voltage is 1 volt, anything above 1 volt will clip.
But but but... we don't care about the technical details! We just wanna know how they sound!
Yes, of course! But knowing how something works makes it easier to understand how it will effect your tone.
When a diode clips the signal more, you end up with more compression and distortion, but less volume. Since this circuit is two clipping circuits in series, if you cut the signal from the first circuit, the second circuit won't clip as much. This is what gives the Muff its harmonic overtones. If you remove the first diodes, almost all of the clipping is handled through the second stage, resulting in a smoother, more compressed sort of sound. If the clipping is only handled by the first stage, you end up with far less compression and clipping... sort of a lo-fi distortion/overdrive kind of sound.
In the VTF, you can consider the octave section sort of an octave-forming clipping section on the first stage. More signal from the first stage results in more clipping from the octave section.
ANYWAYS, TL;DR readers, this is where you stop scrolling.
The diode options are, in order of clipping (least to most):
LED
Silicon (Si
Germanium (NOS) (Ge)
Schottky
Germanium (Generic) (Ge)
Realistically, both germaniums and the Schottky are about the same. The NOS clips a little less, and the generic ones a bit more. Schottky... well... has a different character.
I wouldn't recommend using Germanium or schottky in the first stage. They cut sound a bit too much. Though, having the gain cranked with two Ge stages does have a cool warm tone. I'd think anyone into that wouldn't really be into this pedal for getting those tones, though.
I think the easiest way for me to do this is to go over some combinations that I liked, and if I leave something out, just ask. They're all in the format First stage/Second stage.
Si/Si - Standard Muff configuration. Demos were done with this combo, and basically everything will be compared to this configuration.
LED/Si- More high end raspiness and "crunch"
Si/Ge- Warmer and darker, slightly less volume. Great combo for doom/stoner tones.
LED/Ge- More crunch than Si/Ge and not as dark. Also great for doom or, well, basically anything. This is my favourite combo.
LED/LED- Crunchy, raunchy, loud, gritty, etc. Lo-fi fuzzy distortion.
Si/Schottky- More high end crunch than Si/Ge, and a bit of a more dynamic character.
LED/Schottky- Really cool, interesting crunch.
None/Si- Tons of low end-- almost sounds like there's a clean blend even with the clean blend turned all the way down. Very smooth.
None/Ge- Similar, but more compressed and smoother.
None/LED- Similar to LED/LED, but without some of the crunch.
Si/None- Loud, weird distortion tone. Not much compression. Can tend to "rail bash", which results in a "farty" distortion.
LED/None- More output than Si/None, more open tone. More tendency to rail bash, but not quite as hard.
So, basically, you can see that more output from the first stage means more compression and smoothness on the second stage, and clipping on the first stage generally results in the tone opening up more since the second stage can't clip as hard.
Sorry for the TL;DR... I'll work on a shorter version, but in the mean time, I'll be glad to answer questions or give recommendations for the style/tone you're looking for.
My tests were done with the second proto, a Moser Spawn with Dimarzio Split P/Model J straight to the jack (with a switch, of course), into an Acoustic 150 and Avatar 4x10 (no horn).
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I think I might be member #1 
