I didn't like that the 2nd stage had such a high DC gain. I obtained a 4559* and it worked with that. TL072 is another good choice. The opamp's input bias current creates a voltage drop in R10, which is multiplied by the DC gain of R11 and the MID & BASS pots. This caused the large offset you observed on IC1.2's output. As you said, a proper fix would be to disconnect the left end of R11 from Vref and return it to GND thru a 10uF cap. That reduces the 2nd stage DC gain to unity.
I agree that PRESENCE is wired backwards. It's also extremely touchy below 2 (9:00).
I used ITT GD012 Ge diodes. They are allegedly equivalent to 1N34A. With BURN at minimum and S1 in the center (off) position, they clip at 300mVp-p. With BURN dimed, they clip at 485mVp-p. Input is 200mVp-p at 250Hz. Because the circuit impedance around the Ge diodes is low, diode leakage is not much of a concern. I don't bother measuring Vf at some arbitrary DC current because that doesn't tell me what will happen in the actual circuit.
On my breadboard, I can saturate the 2nd stage if BURN, BASS & LEVEL are dimed, DYNAMICS is set for max resistance and S1 is in the center position. Another solution is to keep LEVEL at the output of the 2nd stage and increase R11 a bit.
* the DC voltage at IC1-7 is 5.00V with Vref = 4.49V.