Good write-up, Sandy.
Allow me to clarify a few items if I may.
C1, C7 & C9 are coupling capacitors. They couple the signal from one stage to another. C1 & C9 are both 22nF and both feed a 1M load (R2 & R8, respectively). 22nF * 1M = 22ms time constant. The low freq corner frequency is FL = 1 / (2*pi*R*C) = 1 / (2*pi*1M*22nF) = 7.23Hz. If you need more bass than that, I'd like to know why.
C7 is a little different because it feed a non-linear load: D1 & D2. C7 is in series with R6, so at least we can say that as long as C7's impedance is lower than R6's, it won't have much effect on which frequencies get thru. F = 1/ (2*pi*R*C) = 1/(2*pi*1K*4.7uF) = 34Hz. So there's not much bass to be gained by increasing C7 either. Try increasing or decreasing C7 and see for yourself
The low-freq response of the Rat is controlled by C2, C3, R3 & R5. There is plenty of analysis of the Rat circuit available on the Web, so I won't rehash it here.
What else... Oh yeah, the FILTER network. This is not a shelving filter. It is a variable freq low-pass filter. The corner freq varies from 475Hz to 32KHz. Most people's hearing cuts off above 10KHz and is completely gone by 20KHz. Knock an octave or two off of that if you're older than 50 or spent time in front of a 4 x 12 stack. Guitar amps & speakers cut off above a few KHz as well. My point is the FILTER pot doesn't sound any different at 7:00 or 9:00. Increasing R7 or C8 are popular mods.
R6 doesn't protect the diodes becuse most opamps, including the LM308, have current-limiting in the output stage. That will protect the diodes from damage. Opamps don't behave like normal opamps when they're in current-limit. R6 is there to keep the opamp happy and control the shape of the clipped waveform when the diodes are conducting.
The Ruetz Mod does not decrease the gain slightly, it decreases it significantly. Which is fine if you don't normally dime the DIST pot. It's a good mod if you want a low-to-medium gain dirt pedal. If you want to run high-gain, then something else is req'd. That's why I introduced the CB mod. I don't know if anyone else tried this before me; I'd be surprised if I was the first. The CB mod preserves the gain structure and allows you to add back in some or all of the bass that was removed by the C2, C3, R3 & R5 network. It's not a subtle mod.
If you increase the DIST pot value, you will need to reduce C5 proportionately, otherwise you will choke-off the treble at high gain settings. 100pF & 500K will cut the treble above 3.2KHz. A large value DIST pot can also interfere with IC1's biasing, particularly so if C2 and C3 are (leaky) aluminum capacitors.
By all means, try everything and find out for yourselves what works and what doesn't. I strongly advise you to change one thing at a time so you don't get lost.