First, try to figure out more about where the clicking is coming from. Does the clicking volume change if you turn up the INT control? Does the amount of ticking you hear change if you rotate the Depth control fully CW or fully CDW? If the ticking level changes when you turn those pots, it would suggest the ticking is coming through the PT2399 or through the dry signal path. That could mean it is your input wire picking up the ticking instead of the output wire, or maybe it is something in the circuit. That might help you isolate the problem.
A few suggestions ---
Sometimes the clicking might be picked up by your power supply or by your guitar (especially a single coil pickup). Try another power supply if you have it and see if that makes a difference. Or try your power supply in a different AC outlet and see if it makes a difference. If you were plugging your guitar straight into this pedal, try putting another pedal in front of it and see if it makes a difference.
In the effect itself, keep the input and output wires from the audio jacks to the footswitch separated from each other as well (my guess is this won't make a difference, but worth a try to see).
And in the dwindling list of other things you could try, you could use shielded wires from the audio jacks to the footswitch. Note you only ground the shield on one end of the wire - easiest to do that at the audio jacks where you solder the shield to the ground terminal.