From your explanation seems that you have a lot of experience debugging electronics, but we can try to add our experience.
- Seems that you can load the signal generator, do you get a "clean" (noiseless) signal when you just play a sinewave?
- Are you able to load any effect, like volume/boost or bit_crusher i.e and get a decent signal (working effect)?
The noise you mention looks like power supply noise, how are you powering the pedal? some usb power levels are pretty bad... have a look at this topic, is mean to be for Ardunio DUE but you can apply it to the UNO: www.electrosmash.com/forum/hardware-peda...-arduino-due?lang=en
I would start looking at power supply noise, keep me updated with your progress!
