Have you checked the resistance from the case of the alt to the frame? Should be close to 0 ohms. You probably have already, but it could be the "master" ground connection could be compromised somewhat and would be prohibiting voltage output of the alt. Also you can check current drain with everything off by measuring current with your meter by placing it inline with one of the battery terminals to see if there is something draining abnormally high. If there is current being drained, and if over 10A, you will probably have to put some resistors inline with your meter as most hand held multimeters only can take up to 10A or so (could fry it if there is no fuse protection in the meter).
Wags