"Dead short" implies no resistance at all. If so, all the wires would be cherry red and too hot to touch. You do not have a "dead short" or the bus would be on fire.
But, you do have something drawing down the batteries. It could be some electrical device that does not go off with the key, or it could be some kind of failure. If you see a negative charge when the engine is running, either the alternator is not working, or whatever the draw is takes more electricity than the alternator can put out.
If you have a portable ammeter with the capacity to take the current of the bus batteries, you could make some tests. If you have a standard hand held multi-meter that only takes a fraction or a couple of amps, you will need a shunt resistor to measure the amperage as voltage drop across it. The easy way would be to use a DC-rated clamp-on meter that clips around the wires and measures the magnetic field.
To test the alternator, put the clamp-on around the output wire, or disconnect the output wire and put the ammeter or shunt in line between the alternator post and the wire you removed. If the alternator draws voltage from the battery with the engine off, it is bad. With external diodes on a high-capacity alternator, perform the test between the battery wire and the diode pack.
To find an unknown draw, put the clamp-on around the hot or cold battery wires, or else disconnect either the hot or the ground wires from the batteries so there is no power to the bus. Put the ammeter or shunt in line between the disconnected wire and the batteries. If there is current showing, the troubleshooting method is to disconnect wiring to the bus's devices one at a time until the meter reads zero. If you have a radio with a clock and station presets, there may be a fraction of an amp drawn all the time for those.
As far as poor alternator output, there are several factors to be measured, the output voltage, the output current, and the load current. If the load is excessive, the voltage will show low and the alternator will appear to have no output when it actually is working as hard as it can. This might be a reason for the discharge on the ammeter if there is a problem draw somewhere. A clamp-on around the output wire would confirm any current coming out. Testing with an in-line meter and the engine running is a bit hard.
If the regulator or alternator are defective, there could be low voltage with little to no load. This too would show the discharge as the batteries and not the alternator are powering the bus.
The other possibility is a bad connection somewhere. We had an almost-new Mercedes/Freightliner that stopped charging, and ran the batteries down to the point that the Allison transmission stopped shifting. There was charging voltage at the alternator output, but none at the batteries. It turns out there was a binding post on the frame behind the fuel tanks where the heavy wires were all bolted together but not passing power between each other until the terminals were cleaned.
Electrical problems require detective work. Good luck.
Someone said "Making good decisions comes from experience, experience comes from bad decisions." I say there are three kinds of people: those who learn from their mistakes, those who learn from the mistakes of others, and those who never learn.