I've been musing about mods for this circuit recently after getting it up and running, haven't tried translating any of my mental mods into the physical world yet, so I'm keenly interested in how you'll achieve this.
Maybe have a gander at Red Beard's Honey Badger, it's Blue Box based and has the octave bypass stomper.
A pound of cure?
How would you ground the base of Q3? disconnect the transistor side of R20 and route it to a switch (and of course then on to either the transistor or ground)? SPDT on-on toggle, or a DPDT stomper with LED indicator on the second pole. I was thinking of interrupting the signal at R18.
An ounce of prevention?
I was also thinking of trying to interrupt the circuit before it can get to Pin 11 of the CD4013, but that would require cutting a trace on the board — relatively easy IF it's a single layer board, but I doubt that's the case here.
Another option would be to lift the pin 11 leg to interrupt it with a switch, no trace-cutting required, but may compromise the chip itself over time.
Simplest way?
Another way to approach it would be to wire up the blend pot to a switch with another external-pot or internal-trimmer. There are pot-swapper PCBs out there if the offboard wiring is daunting (it is for me). So with the flick of a toggle or with a stomp you could change between wherever the blend is set to full-on-fuzz (or full on Octave or somewhere else inbetween). 'Course this isn't where your set blend for the fuzz would be, but if you're cutting out the octave, why wouldn't you have the fuzz on full?
I think this way will be the least likely to pop; messing with transistors in circuit while powered up tends to cause some snap/crackle/pop in my limited experience.
Hopefully somebody more experienced than I will chime in at this point with sage advice.