Hey Flip,
A couple more comments and I'll stop because it seems you are obsessing over things that aren't actually broken. :-) Or maybe it's just a way to get us all to listen to your demos. HA! (I am teasing now, really.)
First, it looks to me like the pickup is wired correctly. It would be hard to do it backwards because the shield peels off and then the center conductor continues 1/4 further onto the board... (See the pic of your pic below). There does seem to be a repair to the 22M-ohm resistor which may have accidentally been lost during the pickup replacement job. And, the solder work on the underside of the board looks a bit ... stone-age. No offense if the service guy happens to read this thread - it is all working!
But what Mica said above means it's still possible your two pickups are out of phase to each other and I can't wait to see what you discover. (You don't need to get the compass very close as the pickup magnets are quite strong. Just see which end of the needle points towards the bass for each pickup. If one is North and one is South you have a mismatch. Cool test!)
Next, the ground wire to the bridge is something somebody probably did in a misguided effort to reduce hum - which more than likely was just coming from the pickups. I think this is a common Fender bass thing but doesn't apply to these basses - or it would have been part of the original circuit. The gang here can correct me if I'm wrong about that one.
Penultimately, you have an old style preamp board with the old style in-line coaxial pickup connectors. The current pickup connectors have the male part mounted directly to the board. There are adaptors available so you can use old pickups with a new board (and maybe vise versa) but since your replacement pickup has been hard wired your rig has already been altered. If you were to order a new set of pickups, how would you connect them? If you got a new board AND pickups, you would still need an adaptor for the hum coil which has the mini coax. And so...
Lastly, If you are planning to send this bass to Alembic to update the electronics package then all of this is moot. Until you do that, flip the phase externally (if that sounds better to you) and just play the thing!! The bass sounds great in all your examples!
Jimmy J
