Have you scrubbed and cleaned your battery terminals (with a wire brush) and also the cables and connections leading to the battery lately?
I would try to see the back of the alternator while the engine is running, to see if you can see sparks. The battery + wire when hooked to the alternator is very close to a ground, namely, the alternator case. Just check to make sure the two are separate.
These are ideas. You may have a loose connection somewhere else. If someone else has had this problem, maybe they could chime in here.