Not charging and short to ground.

Brad.S.19

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Well I tore part of my engine apart this summer to do injector cups, water pump, trans cooler and a few other odds and ends. I got it back together started up fine, the batteries died after a short trip around the block idiot light came on. Did a 40 amp charge till they rreached 12.6 VDC. Started it up again voltalge dropped the alt not charging verified all the connections I had off to be correct snug. I ended up throwing an alt(brand new napa stock replacement) at it still not charging.

Checked my power inputs checked resistance all under .5 ohms and 12+~vdc. The blk/org wire with 2 12g 95 amp fusible links that runs over the fire wall has continuity to ground at the power lug on the relay block by the master cylinder. Checked every fuse for continuity to ground they all have it. Why is this occuring or what may be causing it I wiggle all the wires and connections it did not change a thing. I need some Ideas or where I should go next. I am assuming the alt is fine unlikely two bad ones in a row. I honestly cannot figure out what is wrong with it I am at a loss.
 

Brad.S.19

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I did some more digging and testing, I think it maybe a bad isolator in the box. It makes sense but not sure I do not wish to through parts at it at this very moment.
 

Overdrive

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And your fuses didn't pop when you grounded out?
Disconnect the wiring at the batteries and alternator. Remove the main + feed to your fuse box. Start checking which fuse circuits are grounding out. If they no longer ground out your ground is before the fuse block. If it's stil there it's in the fuse block.
You can't trace a ground with everything hooked up. So by disconnecting you're breaking the circuits apart to narrow down the ground. Start tracing for ground after everything is apart.
 

Brad.S.19

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I switched two of the connections. It was feeding power to the ground on the main power on the fuse box .
 

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