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Tone Pot Lowers Neck Pickup Volume Issue

Did you check if the tone pot lead that connects to the cap is shorted to ground? That would at least be an explanation why anything is happening at all with a disconnected cap.
I will check! I did notice that the neck pot does seem to be a different age than the others, the value is covered by a glob of solder but I’ll try to take a look too.

Will also reverse the leads just to make sure! Thank you everyone, if nothing else I’ll just rewire the whole thing haha.
 
I would take the wiring diagram @Wasnex provided, print it out, and go wire for wire (verifying and crossing off each wire on the printout), ensuring connections are correct. Sounds like components are 'working', just not hooked up correctly.

Did seller declare this, or was this a complete surprise?
Complete surprise! The seller was an older man and the second owner though, so I figured he wouldn’t really know if anything had been changed.
Think I will just redo all the connections and try to figure out why the neck pot looks different than the others.
 
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Complete surprise! The seller was an older man and the second owner though, so I figured he wouldn’t really know if anything had been changed.
Think I will just redo all the connections and try to figure out why the neck pot looks different than the others.
At this point I would take it all apart, check the pots with an meter, and get rid of some of that excess wire when rewiring it.
 
There is no ground wire connected to the jack. The grounding is through the shielding.

This won't solve your immediate problem, but I highly suggest that you add a ground wire from the pot case where all the other black wires converge to the currently unused ground terminal on the jack. Jacks do sometimes loosen, and having a ground wire as a backup for that physical connection means your bass will still work fine if/when that happens.
 
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If that’s the case I can not think of a way how the tone pot has a different effect on each pickup.


Faulty pickup or faulty volume pot. I agree with the suggestion to switch the pickup leads...see if the problem stays with the pot or follows the pickup.

It's possible to have weird intermittent faults that cause components to act like some other sort of component.
 
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That second vol pot (one in the middle) looks like it could have gotten a little toasty. Is it possible it got cooked?
I've done it...
One thing I did and it was a super great investment in wire and alligator clips is to make up a few jumpers with alligator clips on each end. It's super handy for troubleshooting.
If it was me, and I had been troubleshooting for a while with no solution, I'd get 3 new pots, and a new cap and start over. Or at least backtrack and systematically undo stuff until I got to a point where things worked and then carefully rebuild the circuit from there. Temporary jumper connections can be used to try stuff before you solder and make it permanent. - Also, I've owned bases that have front load pots that rely on the mounting plate to provide the ground connection between pots. I'm belt and suspenders, so even if it's that kind of bass, I ground like the first pic in post #9.

Good Luck!!
 
Huh. So for the sake of experiment I converted the bass into a concentric layout (the wiring diagrams out there are so bad lol), and the problem still persists. Makes me think its just the neck pickup "going bad", as the only part I kept from the original wiring was the jack and I made sure to use the ground lug this time.

Guess I'll order some new pickups and see! Thank you all for the help!

EDIT: One thing I did notice is that there were 2 ground (black) wires coming out of the pickups... is that a sign of a stacked pickup? Not sure why that would cause my problem but just an idea.
 
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