Nice work and good call on the shielded jacks!
I had the same problem on my ZPM, so I just cut a piece of 0.5mm aluminium sheet, drilled a small hole for a ground wire, taped it up and slid it between the board and jacks.
It makes everything a bit of a squeeze but the clock noise seems to be gone, even with very high gain.
I like this pedal a lot more now.