I am going to have to print your saga out and read it a few times, just to get some kind of grasp on what you did. No wonder you haven't gotten any replies, yet.
Only you really know. No unkindness meant, here, only sympathy for what appears to be a real dilemna....
In the past, I got myself into such situations by not tagging wires or making at least some rudimentary sketch / schematic of before / after. Not doing that can be a real killer.
You may have guessed that the only way out may be going back to where you were: put it ALL back as stock, then take little baby steps to do your mods. From your narrative, you made several assumptions and guesses. Not good.
Have you got a factory service manual with the wiring diagram? Those things are good in one respect, showing wiring colors, gauges, locations. But there are always mistakes, sometimes pretty serious ones...
Sounds like all of those added grounds (alternator case, xmission hsng, etc) could definitely be causing a serious ground loop. A quickie might be to pull those off and see if situ. improves.
To not go on too long, one last suggestion: when this tech gets confused or lost, I look at a good working unit of what I'm working on to compare wiring, component placement and such. Now, you might have to go as far as the local wrecking yard, but you need to get things back to the way they were ASAP. Looking st someone else's ride or wrecking yard car could really help - but remember that it will need to be same yr, make, model....otherwise differences could make things worse.
Take it slow. You don't need a fire.
Blessings on your work.