If you use both outputs you simply get one pickup per output - you will of course need to use 2 amplifiers.
If you want to use a mono amplifier, just use the bass/mono out out on its own. It sounds like you have the operation under control.
You can test the 1/4" output wiring by plugging stereo headphones directly into it. You should hear one pickup in each ear. If you can do this test, please post back with your results.
For the 5-pin output, you will need to test with another unit as Vince describes, or take it to a service person to test. I can send you a schematic if you need it. I suppose we need to confirm that the 1/4" output is working properly, and then figure if the 5-pin cable or the DS-5 is preventing one pickup from getting to your amplifier.