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The bridge pickup definitely has more output than the neck, and one reason is you can get it closer to the strings. The solution is very simple, crank the neck pickup as close to the strings as it will go (making sure you stop when you feel the screws snug up...any further and you'll crack the pickguard and strip the screw holes).
Then you LOWER the bridge pickup until two things happen: one, the string to string balance will be better (no more "dead" E string and over-hot A) and the bridge to neck p.u. balance will be much more even (with a small advantage to the bridge).
Also, as stated before, playing with the "vintage" knob will give different sounds and output, but basically it should still be a much better balance. These beasts just don't work like the average bass...but that's why we love them!