Looking at the schematic 4.7k would have given you the opposite problem that you have now, that red band on the 47k when compared to the diode and other resistors is surprisingly brown, but anyways...
My last guess is an issue with the switch, I tested this in simulation (albeit without the bypass network) and if S4 stays grounded you just get ridiculous clean signal boosting according to the simulation. Green is signal at grounded diodes, blue is the clean signal from the other branches before it goes into the next gain stage (u3 on my picture) and then red is node Vtone, before the volume control, with the multiple lines representing position of the gain control. So if my simulation is to be believed then maybe check that the switch is switching correctly on the S4 half and if it is then I don't know what else you can do but check continuity with each component in the clipping section and compare voltages with your working unit.
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