"Correct" LED connection to 3PDT

[moogatroid2000]

[/quote]You just permanently shorted the fx input and output across the switch.

Yeah I saw that in my head as I went to sleep. Guess I need to rethink it all.  

If both in and out could be grounded would that make any difference in regards to popping?

[analogmike]

HI,

Very interesting idea about the jack ground connections. But you can prove that will not solve your popping problem by wiring your battery clip black wire directly to the circuit board temporarily. If it still pops, your problem is elsewhere. Try it and let us know if it helps.