Have you checked all the fuses, both under the dash, and in the engine bay? In particular, I would check the VSS/ALT fuse under the dash. If it's out, your speedometer will only work intermitently and it might also keep the alternator from charging the battery. Has it been having any other electrical problems at all? If you've already replaced the VSS in the tranny, I would say it's an electrical/wiring problem.