The G&L MFD P used in the SB-2 uses a single ceramic bar magnet glued underneath each coil half with a copper plate glued on the bottom of the magnet. The only likely “off” things I could think of that would decrease output on this design are a damaged magnet as mentioned above, bad magnet alignment that leaves the magnet closer to one side of the coil, or loose or badly placed adhesive either between magnet and coil or magnet and copper plate that leaves space in between the layers. I have had a number of these pickups in different basses and have had old magnet adhesive give way on one before that mostly just resulted in a highly microphonic pickup, though I’ve never found balance issues as you mention. I would pull the coil out and inspect the bottom to see magnet alignment and glue integrity.
Here’s a pic of the coil-magbet-copper plate stack I stole from a TB classified ad:
View attachment 4465871
Curious how well do the strings align with the pickup in your bass? I’ve had an SB-2 with pretty terrible string-to-pickup alignment from the factory (and mine was a US bass), though I was able to balance the output just fine on that bass with pickup height adjustments. I find that pickup needs a little more clearance underneath for the best performance vs a typical alnico P pickup FYI. I also find the polepieces better at slight tonal adjustment than output volume adjustment.
Also when you say the pickup height adjustments made little difference, that seems suspect- raising the pickup under just the D should make a pretty noticeable difference