Caps like that in series with signal are not affecting the audio. Typically used to remove any DC voltage. This is why " he said, no matter". But if you remove them, do tell if you hear anything different.
This is what David from Audere had to say:
"You want to separate the bridge ground and pot grounds from the green/white wire - the green/white wire is at ½ of the battery voltage
The bridge ground and pot grounds need to go to the grey/white (center pin of the output jack)
The green/white can go to the pickup commons
But since you have coupling caps on your preamp inputs - the pickups commons can also go to the grey/white
And insulate off the green/white (so it doesn't get grounded)
In the present wiring - if you touch the strings to a grounded object you will hear a super loud popping sound
And you are sending static discharges (aka touching the strings discharges your body especially in winter) through the power supply instead of taking them to ground - this can take out the preamp...
David"
The present wiring he is referring to, at first I hooked up everything to ground in one terminal point (bridge, black pickup wires, cavity and control plate.) So, upon his advice I separated the bridge and other grounds, soldered them to output ground (grey/white) and left pickup grounds (black) going to the green/white.
There was a definitive difference in tonal quality before and after. The first way I hooked it up was "punchier" and "hotter" but nothing off about it. Now it sounds more even I guess. This MX Mexican Fender fretless neck has flame running all through the maple grain and an excellent rosewood color. Super transparent with the Thomas Brantley pickups.
No knobs yet and that makeshift control plate is serving the purpose of wiring up to play it before I redrill the five hole line-up on a gold 3-hole plate.