@Manny - I agree that there could be cross-talk in the switch, but that can't be whats causing it. Since I switched my LDR to in-line I haven't had anything but the negative battery lead on my footswitch and thats like 3 days ago...
@dead - I'm going to try a regular yellow to see if it helps. I tried the circuit with just the red LED that faces the LDR and without a rate LED at all and still got ticking. I took the signal section out of the pedal today and played around with moving it around in relation to the timer circuit. Seems like I get the most ticking when my signal ground and power ground wires are close to each other - within 3 inches or so I get ticking. I also noticed that the ticking is reduced to almost nothing (usable levels) when I touch the battery with my bare hand, even with the pedal setup the way it is.
I'm probably going to nix this circuit and finish my EA to sate my hunger and call my tremolo project done, though I plan on keeping this circuit going until I straighten it out. I was thinking shielded wire for the signal section, reworking all the wiring in the box, swapping the blue LED for a regular red or yellow and probably socketing my LDR so I can try a few more out to see if that helps. Of course, until I can get parts for the EA tremolo (next Monday) its still open season on this circuit so any more suggestions are more than welcome.