Here's something to check. In your second photo, there's a short red/white striped wire that starts at pin 4 of the XLR (this pin is the 4th one counting clockwise from the black wire). On the 1/4 output end it should be connected to one terminal of the jack with no other wires. It's hard to tell in the photo, but it looks like it's soldered together with a yellow and black wire, but this may just be the camera angle.
This is important! The 1/4 jack is much more complicated on a Series bass than any other instrument that I know of. In addition to the regular tip/ring/sleeve outputs for stereo outputs and signal ground, it's also got two switches that are flipped when you insert the plug. One of those switches turns the battery on when you insert the plug; the other switch effectively cuts off the external 20v power to the onboard electronics.
External power on the XLR5 connector are the two striped wires on pins 4 & 5. It looks to me like the red/white stripe wire from pin 5 is connected to ground rather than the 1/4 jack switch (this is the normally closed or n.c connection of the jack and may be marked as such).
If it were miswired like this (very easy for the tech to do this), then the external power would never be activated, even when there was no plug in the 1/4 jack AND the external power supply was connected. And you'd have exactly the behavior that you're seeing.
I believe you can probably do an easy test before you dive in there. Connect the DS5 to your amp and bass as normal. I think if you stick a plug in the 1/4 jack (the other end should not be plugged into anything), then you'll probably find that the stereo out will work. The reason that this is the case is that the power will be supplied by the 9V batteries instead of the external power supply. As Dela mentioned above, it looks like the output portion of the wiring mod is OK.
In the grand tradition of giving an important warning after telling you to do something, I should suggest that for this test it's actually better to stick the plug in the 1/4 jack FIRST, then connect the XLR5 (but again, you leave the other end of the 1/4 cable unplugged). When the 1/4 plug is inserted there will be a big thump when the electronics powers up. I explained it backwards because I wanted to make sure that you're listening to the DS5 outputs, not the 1/4 one.
If the red/white striped wire is connected to those other wires (which are the common ground), then you will need to extricate it from that tangle and... uh... connect it to the right place. I'm not exactly sure where that will be however. If you know how to use an ohmmeter or continuity light, then you need to clip one probe on the jack pin that the blue/white striped wire is on, then find the terminal which doesn't have continuity only when a plug is inserted. There will be only one pin on the jack that acts like this.
As Dela pointed out above, you *really* want to improve the insulation on the legs of those resistors. If they were to touch any grounded part of the instrument, then you'd lose signal from that pickup. If you look at the resistor running to the red wire on the XLR, you'll see it passes very, very close to a big metal tab sticking out of the back of the connector. Yup, that's the connector's grounding lug. If you bump that leg of the resistor over to touch the lug, you'll hear one pickup go away. The same thing would happen if any of those uninsulated legs were to touch the back plate or painted portions of the control cavity.
And yes, the grounding flag is the common ground point on the 1/4 jack. From a practical standpoint, it probably would have been nicer for Alembic to bring all five of those ground wires to a common point off the jack, then connected from that common point to the output jack. Having good integrity of the grounds is very important, and wiring direct is good practice for high performance, however, it makes the job of changing the output jack much harder (no tech would take this job on at the side of the stage!). If the red/white wire was incorrectly soldered to the common point, then your life will be much easier if you cut it off rather than unsolder it, so you don't have to deal with resoldering the other five wires.
If the red/white wire is sitting on it's own terminal and isn't shorted to anything else, then the switch is probably bad in the 1/4 jack and you'll have to replace it (gulp, that would not be fun).
Good luck, and tell us how it turned out!
David Fung