Another noise thread

Hi all, I just built a Pedal Pi and am having issues with noise. The main issue is I am getting lots of 'crackling' noise when playing notes, either individually or in a chord. Also I noticed there seems to be a lot of high end cut off the guitar as well, as well as being much softer volume

If I play directly via the foot switch it is fine.

I have tried the following:
- Resoldered all joints,
- Disabled wifi
- Tried two different power supplies and a USB pack
- Tried various settings on the VR

I noticed C5, while branded as a 270pF cap actually measures 370pF out of the circuit which could explain the lower freq cutoff so I will try to replace it but I can't figure out the crackling.

I have attached a wav file of myself playing individual strings (in a zip file as wav is not allowed), directly then via the 'clean' effect. Then the same again using chords. It is a bit hard to hear the cracking until the end as the phone has filtered out some of it but it should give some idea of what it sounds like when enabled.

Can anyone give me any other suggestions?

Thanks in advance