Follow up. Problem/s solved.
After going through ALL the connections I have, with Tim's reccomendations and help, pretty much rewired the ENTIRE battery box. Turns out that my van was hacked at some point in it's life and ALL fusible links were removed, and wires re-routed, wire nutted and hap hazardly scabbed together with crimps creating bad connections due to grease, dirt and improper installation.
After discovering that and a faulty ground, the culprit turned out to be a mixture of a few things. First, the ground to the battery thats runs to the block/ subframe had began to fail. This was replaced where it is bolted on the subframe, just adjacent to the battery compartment. Where I was getting random ohm readings (sometimes good, then above 30 ohm's/ resistance to ground) I now have a solid 0 ohm reading.
The fusible links were cut out at some point and all needed to be replaced.
Side note on fusible links: Toyota has a standard of upsizing wiring at least a gauge size in most of thier vehicles, thus the FL is sized according to the gauge of the wire to be protected.
A quick break down of rating would look like this:
A 12 gauge fusible link is 3.0 sqmm
A 14 gauge fusible link is 2.0 sqmm
A 16 gauge fusible link is 1.0 sqmm (note: Toyota uses a 1.25 sqmm rated for roughly 26 amps, it is hard to find outside of the dealer- upsizing to a 2.0 is a 7.5 amp difference at 33.5 A)
A 18 gauge fusible link is 0.85 sqmm
A 20 gauge fusible link is 0.5 sqmm
And so on.
I spliced in new FL's for the 2.0 rated circuit (8 gauge wire) and the 1.25 rated circuit (10 gauge wire) and routed directly to the battery terminal. The white voltage sensing wire had a weatherproof fuse carrier wired inline with a 15 A fuse installed. The sensing wire at .5 sqmm is rated at 13 A, so it was a rather moot point to hunt down a fusible link for this function.
The results were as expected. Charging happy at 14.3 volts consistently at the battery and 13.4 volts across the harness points I could test. Anyways, all cleaned up, connections greased w/ some dielectric and ready for years more service!
Attachment 8123Attachment 8124Attachment 8125Attachment 8126
Cliff notes: For an over charge condition from the alternator, check and verify these things:
Plug from harness at alternator is sound/ not defective.
Regulator is functioning properly (wise to check wiring first!).
Verify Fusible Link .5 is present and working properly, replace if faulty or missing with either a NEW FL or a 15A inline fuse on 14 gauge wire.
Verify ground connection to battery and frame/ engine locations.
Verify charge circuit fuse is good.
Happy vanning!