Strange Electrical Behavior (1 Viewer)

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13.2 is good That means your Alt is working
 
The journey continues, but I've made progress...

I grabbed a compatible alternator with internal voltage regulator (searched for 1986 Land Cruiser alternator and ended up with this one, for future searchers). The thinking is that this eliminates a variable from the equation. To check things out I just bypassed the wiring harness to the alternator. I wired the lug straight to the battery and the reference voltage to the alternator as a jumper from the lug. The IG source just came from the old coil wire since it isn't being used otherwise. Started it up, and BAM, 14.2V across the battery.

So, as it stands, the truck is functional, the battery changes, and so far the misfire hasn't come back. I'm still monitoring, though.

BUT...

My ammeter isn't functional since I'm not running through it on the way to the battery. So, since I verified that the new alternator+voltage regulator combo is good, I decided to hook up the original wire to the alternator lug. This is where I made a discovery...The voltage across the battery was back to 13V. I measured from the alternator lug to ground and it was 14V. Obviously something is amiss in that circuit.

So it's good news/less-good news. Anybody have any tips for tracking down the issue? I think my first move is to remove the "stop", "headlight", and "tail" fuses to see if it gives me any clues. (This is all assuming that I'm reading the wiring diagram correctly.) I suspect that my headlight switch may be the problem.
 
OK. More data...

New battery installed. ...and drained overnight.

Any time the battery is hooked up, my ammeter shows a small discharge, even with the key off. I've verified that the needle zeroes out with the battery disconnected. I removed all the fuses. Still discharging. I removed the fuse box altogether suspecting that maybe the box was grounding out. Still showing a small discharge. I've also verified that the resistance on the wire that runs from the back of the alternator to the battery(+) is near-zero.

At this point, the only things hooked up to the charging circuit are the alternator (new), ignition switch, ammeter, starter, and battery (new). It seems like the only thing that could possibly be happening would be through the starter, but I'm open to/hoping for any suggestions or similar experiences.
 
Sunnuva...(shakes fist)

@charliemeyer007 gets the gold star for calling it.

I detached all the things hanging off my positive terminal and tested each with my ammeter...When I got to the charging wire I got -2.7 amps. As soon as I removed the wire from the alternator end it went to 0.0. Amazing. Replacement should be at Napa in the morning.
 
Yes even "new" can be bad, and re-manufactured stuff is hit or miss as far as quality control.
 
Only problem is that this doesn’t explain the voltage difference at the battery when I run a line directly from the alternator to (+) vs hooking up the original charging wire to the back of the alternator.
 
Update:
Got another 60-series-compatible internally-regulated alternator installed per @Coolerman 's directions. Works like a champ. Figured out that the voltage drop between the alternator and the battery is because of the long run between the two. Nonetheless, my voltage at the battery is higher than it was before all of this, and my wiring situation is much simpler now.

Now for the fun part...After all that, I still have a decent intermittent misfire. I believe I've narrowed it down to the pickup coil being uneven strength - and particularly weak on one specific cylinder. After discussing with the nice folks at Performance Distributors, I sent the unit back to them for assessment. Will update when I run that one to ground. In case you're interested, here's a video of what I found when I took the distributor out:
 

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