Ok, not charging is one thing. A drain overnight is another. It is possible the same damage could be causing both.
Chasing intermittent electrical problems is the hardest flipping thing. Having good tools for chasing the problems can save hours, days even. There are jury-rig ways of finding opens and shorts like using a compass, but learning it on a hard problem is nearly impossible. My suggestion is bite the bullet and get the best tools to do the job, then you have it for years to come.
here is quickest search to pop up, maybe look for a better price, but nothing out there gives faster results for someone that doesnt have a decade of chasing them.
http://www.tooldiscounter.com/ItemD...3Uw07FKL2MK27bTTi2HRlNCF9FZAS4ETNhxoCRuvw_wcB
You can try having someone watch the gauge while you go around shaking the wire harness. When you shake an area and the gauge starts being affected, tear into that part of the harness.
Adding more wires to bypass can be done, but you have to abandon the damaged harness area. Otherwise if a short is still there you can just catch the harness on fire. Ive seen many a rig burned to the ground over this. Once you supply backfednpower to a circuit that no longer blows a fuse and quits feeding- there is no safety anymore.
If you absolutely have to run temporary wire to bypass, disconnect the battery every time you shut off the truck. Have a fire extingusher next to you in the cab. Be ready to disconnect the battery at a moments notice.
As for where to look for the problem, you need to follow the harness from the battery to each end of the charging circuts.
If I'm understanding you correctly, the drain only happens when you connect a pigtail to jumper the alternator? If so, that is normal. The alternator will draw 3-5 amps with it fielded and the engine not running. Another warning, DO NOT DO THIS FOR MORE THAN A MINUTE. Otherwise permanent damage can be done to the voltage regulator as cs-130 alternators require a 35 ohm resistor be installed in the field wire(it's part of the cluster if it has a charge warning light). The voltmeter has no control if it charges or not. You need to do some checks here to see whats up. You'll need a test light here to go any furthur, but they're simple checks. First make sure the large cable is receiving battery positive and in good shape(no burns in the fusible link). Next step is to check the alternator plug. You only need 1 wire if I recall correctly to make cs-130 work, and thats the trigger wire. There needs to be a 35 ohm resistor in this circuit as the regulator backfeeds current, and a direct connection will damage it. But the L terminal in your plug should have positive voltage present with the key in the run position. Insert your test light into the L terminal in the plug, and it should light up when the keys on. If it does, the circuits working, if it doesn't you'll need to find the break in the harness or check to see if the resistor in your cluster is burnt.