Here's a couple of things you should check - first, confirm the exact part number on the switch. You'll momentarily lose all output when you have the break-before-make switch instead of the make-before-break switch that you want which you may perceive as a pop. If you turn a switch like this very slowly, you may be manually forcing both the before and after positions into contact at the same time, which makes it into the right kind of switch.
Second, when you get a loud popping noise in a system with active EQ, it's because you interrupted power to the preamp circuit while switching. It sounds like your plan had a pair of filter circuits, which are active preamps powered from the batteries. They have a DC power supply wire that's coming from the batteries (however many there are). The +V power must not be interrupted at any time and shouldn't be routed through the switch.
The trickier part is that the -V or power ground from the batteries can't be routed through the switch either. Interrupt either line and you'll get an enormous thump at the signal output.
In one of her early responses, Mica noted that only the hot leads (center of the coax) from the pickups go through the switch. Also, all the pickup grounds (the mesh shield from each pickup) join at a common point which is separate from the battery -V or battery ground. The output pole of the big switch is the +signal input to the filter board. The pickup common ground is the -signal input to the filter board (and doesn't pass through the switch).
In your design pictorial, you're doing something a little bit unusual which may also be part of the problem. In most instruments, the volume controls are wired immediately after the pickups and before any EQ or filter boards. In your case (because of the pan pot, I guess) the volume controls are wired after the EQ board. There's nothing wrong with that, but it does make things a little trickier.
The same rule about what gets switched and what gets grounded together applies here, but you have to remember that the post-filter volume pots need to be grounded together, but not together with the pre-filter pickup grounds! The pan pot is pre-filter, so it needs to be grounded in the same common group as the pickups and switch, but not with the other volumes. As an adjunct to this, on most instruments this means the resistance value of the pan pot and volume pots will be different. Because the panpot is living on the passive side of the circuit, there may be some interaction effects (like treble loss) when you treat it like a blend. Fixing this would require a change in the circuit design (you need to have linear preamps immediately after the pickups and before the switching matrix to eliminate the passive interactions).
Although you may not enjoy the tech bill, you might consider working through the wiring incrementally to assure that everything really is working OK. For instance, you can wire up the pickups and panpot, then take that output directly to the output jack. This is a totally passive setup, so there's no battery, power switching, or grounding weirdness (of course, no filters or volume knobs either). Next, add in the filter boards with the power wired directly to the boards (no switching in the jack). After that, add the post-filter volumes. Finally, add the power switching. You'll at least be able to get a sense of how it will sound at each step along the way.
To properly maintain power separate, you really want to create a pre-filter common ground for the pickups, switch, panpot, and instrument shielding. For the power side, you want to wire the filter power supply boards point-to-point from the V+ and V- lines to the batteries, and use a special output jack (like a Series jack) which has dedicated independent power switching. This will keep power separate from signal and also keep you from interrupting the active EQ power.
The reason that you get a big thump if you interrupt power is that the active preamps offset the signal zero point to half the supply voltage. For instance, if you have a 9VDC power supply, the preamp will amplify it's input signal over a range of +4.5V to -4.5V. When you aren't playing (no output signal) the zero point is +4.5V relative to the input signal. If you interrupt the power supply, the output drops from zero being at +4.5V to zero really being at zero. That is an enormous thump, basically as loud as your amplifier can produce.
You want to solve the thump problem by making sure the power is not interrupted. You can reduce the problem with a big capacitor between filter output and ground which filters out the big thump, but this is a low-pass filter which will affect your tone as well.
The more I think about this, the more I think you probably will need to re-examine the circuit to get what you want out of it. In particular, I think it's unlikely that the pan pot will do what you want it to do without buffering the signal from all three pickups before the switch with a set of linear preamps. Doing this will mean that all the wiring in the control cavity will be back to common ground and simpler to understand and debug.
Good luck,
David Fung
