You need to check for ground loops. Here's the deal, if there is wires connected to the bottom of your pots, and your guitar is shielded, you have created a ground loop. More than one. Modify your wiring to account for the pots being grounded to the shielding, then take 1 wire off the shielding to merge with the audio grounds, then out of the cable. This fix will make your guitar even quieter, as it will be fully shielded from interference, and ground loops. I can show you my wiring if it would help.
Noise gates work well when they track the guitar signal. My ISP Decimator 2 G-String does NOT cut off sustain, at all. It just ensures when the signal is off, the noise is clamped. This does not reduce noise while playing but it certainly ensures everything is quiet when your guitar is muted, and no sustain is affected by the gate.