C 3, R1 & R3 form a high-pass filter. Q4 is an emitter-follower so we can assume its input impedance is much higher than R1. R1 in parallel with R3 is about 39K. In stock form, C3 is 47nF. That makes the high-pass corner freq 87Hz. Low E on a Bass is 41.2Hz. 100nF will move the corner freq down to 41.1Hz and let all of the fundamental thru. If you want to let the thump from the subharmonics thru, then go even bigger on C3, say 470nF.
While you're at it, you might want to fatten up C7 a bit too.
Has anyone else noticed how much this circuit resembles the Tone Bender Mark 3? Apparently it's possible to build a PNP pedal without resorting to a charge pump.