Linear and Logarithmic Potentiometers
No that's not the problem. Putting the wrong potentiometer in will just have the effect that most of the control seems to be over a restricted angle of the pot with very little change occurring over the rest of the travel.



Figure 1. Tracing the straight-through signal.

Finding the fault should be easy enough using a multimeter on continuity test.


Test from 1 to 2.
Test from 1 to 3.
Check that you have continuity to 4 alternating off with each switch press.
Test at 5 to check the loop integrity.
6 should also alternate on and off with the switch.
Check at 7 and 8.
Finally, there should be a ground connection to 9 but this may be done through the metal box.


Report back.




  I did ... add a ground wire to the output and that fix it 100%. I've been looking at the output the entire time wondering why it only had one wire attached. I dismissed this as the issue though because I could hear the fuzz effect fine ... strange.


The fuzz signal is amplified so that and some stray capacitance between the circuit and the guitar lead shield may have been enough to give the impression of working. Let's hope you don't decide the ungrounded version sounds better.