There have definitely been a handful of factory wiring mistakes on G&Ls, particularly on the pickup switches of the 2000/2500 basses. My old L2500 came from the factory with some of the wires on the coil switch swapped between pickups (so that Series mode had one coil from one pickup running through one coil from the other for example). Lots of wires on there to mix up I guess! To me it wouldn’t be worth shipping back just to swap a few wires, but YMMV (I was planning on doing some electronics mods on mine anyway).
...and lowered the pickups and bass & volume controls, right? (not to preach or anything, just my experience with them)
Hmm- it might be worth it to try to reflow solder joints to begin with. A weak solder joint could cause issues. Also check that all the switches are switching cleanly- a funky switch that makes intermittent connections or sticks between settings can cause issues. Also (hard to do if it is totally intermittent), but disconnect the battery and check whether you still have issues in passive mode. The preamp in G&Ls is actually always connected to the signal input and so can cause issues even in passive mode (I never used my preamps on these basses and always left the battery out for this reason). An intermittent battery cable or stereo jack could definitely cause these issues. These kinds of jacks are failure-prone, especially if you ever use any cables with larger diameter plugs (like Monster and Planet Waves) that can wear them out faster. See if jiggling/twisting the plug in the jack causes any issues.
