Deluxe Electric Mistress Clock Noise Question

[ddavis20341]

I just finished a project rehousing an early 2000s big box Deluxe Electric Mistress into a smaller enclosure so it could actually be used on a pedalboard. Everything went smoothly, but I noticed that when i turned it on there is WAY more clock noise than there ever was before with this pedal (which was normally very little). It kept getting weirder from there, with the noise sometimes disappearing depending on how I jiggled some wires, and the noise also coming through when the pedal was bypassed as long as the power supply was plugged in (the same power supply I used with the pedal before rehousing - an original EHX supply for this pedal).

This makes me think there is some sort of grounding issue/cross-talk thing going on, since it shouldn't be coming through with just the dry signal. The clock noise also has more of a "thunk/tick" kind of noise to it than it ever had before, which was usually just the standard swooshing hiss thing going on. Everything about the pedal is completely the same as it was (just pulled the circuit board and everything with it and put it in a new enclosure), except for the switch wiring and an LED. I followed these instructions for the new wiring:
http://www.harmonycentral.com/forum/forum/guitar/acapella-29/1681331-

Anyone have any idea what to do? None of the trimmers were moved either in the process, I have pictures of their locations before. I can post pics and voltages if that would be a help. Thanks.

[somnif]

One thing that could help is to use shielded wire for the Output (and make sure to ground the shielding). Shielded cable isn't super cheap, but it can do amazing things in the right applications.

Its also possible you are having some grounding funkiness. Do your jacks make metal-to-metal contact with the enclosure in some way, or are they plastic jacks (or a painted enclosure, or something similar).