3/. I think that connecting R18 to 0V (AKA Ground) is wrong. I think it should be connected to the junction of R29 and R30 (or anywhere along the tracks that connect to that point).
This is not "wrong", as this tonestack is based off the big muff tonestack that was developed in the early 70's and has been successfully implemented in thousands of pedals since. That old tonestack has it's issues with impedance and signal loss, but Keith found it to be a good match in the circuit (probably why the gain of IC2b was bumped up a bit). However, when running the pedal at 18 volts, referencing R18 to 1/2v instead of ground, as you suggest, is probably an excellent idea.
Just to boil it down further, this circuit was designed to operated at 9 volts. It was thought that running it at 18 volts would be fine, for reasons that have already been outlined, but it's looking like there are issues with running the circuit at that voltage. It was my understanding that there were plenty of these kits being run at 18 volts over the last couple of years, and that we were seeing something new in the latest batch of kits with these 3 recent builds that were having problems at 18 volts; but it's looking like my understanding was incorrect as we've had 2 moderators verify the same issues on their builds at 18 volts. HOWEVER, just to try and keep this on track, this particular thread is really about the OP's issue with distortion in the wet signal path, and more specifically on the output of IC1b. The OP should be getting a new brick from BYOC soon, as we think the problem may be in his particular brick, since IC1b cleaned up when the brick was removed. (some of this stuff was handled offline)