I have the negative battery lead going to the footswitch first for bypass. Since I had the in/out tied together for the LDR bleed to ground, all I had to do is switch the 555 on or off for bypass. I admit that I haven't tried the circuit without the switch in it, but again, I don't see how it would make a difference.
I'm thinking it might be the way I have it laid out in the enclosure. The thing that has me vexed is that the signal section and the timer section aren't connected to each other at all. Its basically two different circuits - the 555 circuit with both LEDs and the signal circuit with the LDR, connected only by the light coming out of the LED...
... And now for a gut shot...

Not the most beautiful thing in the world, but likely not the worst you've ever seen either. The PCB at the top, the LED and the LDR are hot-glued in, but not electrically connected to the enclosure. As you can see the input comes in and hits the LDR then goes straight to the output jack. (brown to the LDR then white from LDR to output jack) The signal ground goes straight from jack to jack. (green wire across the jacks) The pot on the right (from this view) is the speed pot and the depth is on the left. I added a couple small resistors (47r) in series with the pots to slow the maximum speed (so the LED will not go solid with the speed at '10') and so the red LED draws a bit less current, allowing me to use a blue LED for a rate/indicator.
I may just take it all out of the enclosure to see if I can get the ticking to stop by separating both circuits by a large area (think 6-8 inches or even a foot). Even so, if that stops the ticking, I can't put it in a reasonable sized enclosure with that much space in between them...
