If it were a VAN, I'd say it would be stuffed behind the brake booster.

The fusible links look very similar to regular wire.

http://www.whiteproducts.com/fusible-faqs.shtml

Also the voltage regulator must be grounded properly. This is done through it's case but some have run an additional wire right to the battery negative to insure a good ground.

 

At this point as it clearly is not charging, I would remove the alternator and voltage regulator and take them someplace that can bench test them for free (Autozone).

If these both test good, it really has to be in the wiring.

In the meantime I strongly agree with Landyacht and recommend using a good quality battery charger to put a full charge back on that battery as soon as possible. Allowing a standard lead acid battery to fall below about a 60% charge (11.5 volts) even once or twice will ruin it.

 

This chart is pretty accurate as to battery state of charge when the voltage reading is taken when the battery is rested. Meaning several hours after the battery has been either charged or discharged, NOT while it is being charged or discharged.

Your continuity checks on the charging circuit mean very little when there is no current passing.

Check the voltages on the back of the alternator with the engine running.

If they are the same as the voltage taken at the battery, then the field wires from the regulator are faulty somewhere.

If the voltages are in the well above 12.8 at the alternator, and below that at the battery, it is the wiring between alternator and battery, and most likely the fusible link.

 

Sorry, I must have been really tired. Thanks for posting the voltage chart.

Anything reading below about 12.25 volts means you are doing permanent battery damage. You can only cycle it that low a couple of times as you will lose 25% battery life every time you do it.

 

Thanks everyone, but I just went in and re-wired the charging system and bought a different alternator and regulator from a different store instead of Checker or Autozone, so far no problems yet, although I had to replace the coil since it was so used to running off of 12 volts instead of 6, so it wouldn't stay running. One thing after another.