Just a post about the problems I encountered with putting my Muff in the loop of my Boss LS-2 incase it helps anyone else who encounters the same problem.

My setup uses a Boss LS-2 Line Selector to switch between my clean signal and my pedalboard and noticed that I was getting loads of noise and hum when my pedalboard loop was on. I went through a process of removing pedals one by one from the chain and found that the culprit was my EHX Big Muff Pi. It was creating hum even when bypassed and after a google I found that it was because of the many buffers inside the LS-2 circuitry (please correct me if this is incorrect!!).
Anyway, by placing the Muff before the LS-2 (guitar > Muff > LS-2 > amp) the problem was sorted and now I am free of hum
Considering making my own loop pedal without buffers now.

I hope this helps anyone else experiencing a noisy fuzz and loop combination!