I would look for obvious noise sources in the setup - room lights, breadboards, jump wiring, the particular wall socket you are using (some can be quite dirty for audio), etc. It's possible the noise will go away once it's PCB built and everything is shielded in an enclosure. Also, stick a couple 470uF caps and a 100n film cap in parallel to decouple the main power supply if you haven't already.
Also, maybe disconnect any pedals in the loops one by one to see if the noise level changes.
Also, maybe disconnect any pedals in the loops one by one to see if the noise level changes.