I bought a PRS SE Dave Navarro off of craigslist, and the neck pickup is so quiet it's almost impossible to hear. The guitar itself is like new, practically unplayed, but I have to turn my amp (Randall C-50) up almost all the way to hear the neck pick up. Needless to say, switching through the 3-selectors is worthless and I can only play on the bridge pickup. I opened it up and checked for loose wires/ bad soldering but couldn't find anything. I also tried raising the pickup, to no avail. There is only one volume knob for both pickups, so the volume knob isn't the problem.

It's the same for playing clean or distorted.
i know you looked at the joints, but i would reflow them. it doesn't take long, and that way you know for sure that you know its not the soldering joints.

get some deoxit and clean the pots, switches, and jack.

i know, generic recommendations, but worth doing.

i think i would bet on a bad switch. i had that happen to me once.
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youre just being a jerk man.

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After you've checked all the connections, it's possible that the coil wire has been shorted out. I've seen this happen with a guy who used steel wool on his frets. The shards of steel wool are pulled into the coils by the magnets. The shards rust within days. When they rust, the crystals of ferric oxide form and expand and can pierce the very thin enamel (usually) coating/insulation on the wire. If nothing else, this allows the copper wire to begin corroding, and it also forms crystals that expand and pierce the insulation not only of its own coating but that of the wire next to it. Next thing you know, you have a coil exhibiting partial shorts, loss of volume, strange sounds, etc.
Check the switch first! It's probably not making adequate contact when in the neck position. The switch probably spent a lot of time in the bridge position, pushing apart the blades that connect when you flip it to the neck pos. I've had the same problem with my SE Navarro (great guitar, btw! One of my main gigging instruments!).

If you're careful, you can bend the blades of the switch slightly so that they make better contact.
Thanks for the advice. I don't know anything about soldering or reflow and all that, but I may take it in to get looked at. I'll check the switch again, because when I tapped the wire it seemed to have strong output, but it just wasn't making it to the pickup.