Maybe I did not understand the problem (I do not speak English I use translators and I'm a little silly too.
Is it the tempo led that brings the tick or the circuit?
On the circuit I actually have a tick but that is that of repetition and perso does not bother me because I do not use this pedal live high volume, against the led it does not bring me ticking I will say that it reduces this famous tick.
I noticed that with the led on, the deph has bottom and the neck pickup coupled to the bridge pickup I have very little ticking (it seems suffocated).
For separate GND I did not understand everything because in the end you have the GND case so everything is finally connected no?
here is what I did, I do not know if it will help you
I hope you find a solution