I then change the R3/470ohm to 1k and voila, I get 1-500 gain, with 3-159 lowpass rolloff and a high pass going from 13khz(no gain) to 2.7khz(max gain).
You had me a little confused there for a sec, because of your terminology, but I think I get it now. Changing R3 from 470R to 1k will make the min resistance on the ground leg 1k, which, in conjunction with a 1uf cap, will give a
low-end rolloff of 159hz at max gain. This would more properly be referred to as "highpass", since it permits content above 159hz to be amplified more (it IS a rolloff, not a brick wall, after all). NOTE, however, that whatever this RC combination does to low-end rolloff and gain, it does nothing to HIGH end rolloff.
Leaving R23 (3.9M) intact still permits a gain which is (on paper) ridiculously high. In conjunction with 120pf in parallel capacitance, the
high-end rolloff this produces starts around 340hz and attenuates more above that.
My feeling is that you need to start with the bandwidth of the clipping stage before knowing what needs to be done to the tone stage to "idealize" it. Again, if it were me, and if my goal were to smooth out the sound a bit, I'd reduce the gain of the clipping stage, and hoist the high-end rolloff. In some respects, this circuit cries out to be turned into a Distortion+. How could you do this? Easy. Change the 3.9M resistor to 1M. Change the 120pf cap to 47pf. That will set max gain at 1001 (min at around 3) and high-end rolloff around 3.3khz. Lastly, eliminate D1 and D2. I suppose the dual sets of diode pairs one often sees in circuits like this serve a purpose, but it seems odd to clamp the signal in a gain stage at an amplitude set by diodes, and then feed that output past another pair of diodes with the same clipping threshold. Somebody needs to explain to me how this yields any appreciable change in degree of clipping.
Far better, I would think, to replace D1/D2 with a back to back pair of red LEDs. These would have a higher clipping threshold, hence produce less (and some say smoother) clipping in the gain stage. Most importantly, though, the output of this modified stage would be hot enough to yield additional clipping from D3/D4. My guess is that this combo will start to sound a bit like a Boss DS-1, albeit with a different sort of tone control.
Re: C8 If you jumper it, then at one extreme of rotation, that path will be a zero ohm feedback resistance, making your tone stage a unity gain op-amp and having NO effect on tone (as well as no boost, which it normally has a bit of). Better, then, to
lift C8 if you want to monkey with the tone, to bring the circuit back to the topography we saw in the first circuit fragment you linked to.
Finally, the schematic you link to shows a rather interesting switching scheme. Normally, the "flip" and the "flop" of a flip flop are used to alternately lift or complete the path of the dry and effect signal to the output buffer. You will see here that the two FETs used for switching are tied to the same part of the flip-flop, so that the two FETs both go high and low together. How does this switch? When Q1 gets turned on, that provides a low resistance path from the input buffer (U1a) to the output buffer (U1b). When Q2 gets turned on and goes lowe resistance, this forms a low resistance path to ground in conjunction with R9 (220k), that makes up the ground leg of a voltage divider formed by R4 and Q2/R9. So, in bypass mode, it gets easier for the clean input to make its way to the output, and harder for the much of the distortion signal to get to the output. My guess is that you may still hear some "hair" from the distortion even in bypass mode because that attenuation is not perfect.
There. That's enough to chew on for a Sunday morning.