I may have the exact same problem as you Exuro89, and I believe we are in the same boat.
My left channel is caput; it initially destroyed my speaker as well (nice burnt smell). Right channel works great, Din's been tested and headphones work great on both channels. I replaced both right and left channel fuses.
When i plug the wires into the left channel pos/neg, the neg(-) sparks brightly and the speaker, even on 0% volume, hums very loudly. I'm an ubernoob at wiring and resistors and capacitors and transformers, so I don't actually know what this means.
While my circuitry panel doesn't have any wires sticking out as yours does, mine appears completely disgusting: https://lh4.googleusercontent.com/-9WL4-rCaRCE/TjgwnpF5FKI/AAAAAAAAACk/f-jwbRP1bp8/s512/2011-08-02%25252012.12.53.jpg
I'm at an utter loss of what to do besides search for someone with a blown subwoofer but working amp/circuitry and switch them out. I'm more than open to ideas and suggestions.