Your battery and starter are (stong) good. If you look closer to your second Video you can see a blow by smoke coming out of the bottom
of the #4 intake boot (mis-firing) @ 0.18 sec.
Have you check your ignition Timing?
As Scirocco said, the cranking speed and vigor seem really good. Keep trickle charging the battery to keep it topped up.
If it doesn't start from the amount of cranking in the videos, then there is definitely something else wrong. It could just be no fuel. You should be on prime. The heinous sound is just backlash in the primary chain due to irregular firing. It sounds almost like it is only running on two cylinders... and not good at all on those two.
Like Scirocco said, I would be looking at electrical issues first since you did so much electrical work.
Take out all four plugs and look for spark. Also check timing while the plugs are out with a timing light. That will show if the timing is at the wrong time, even if the bike is not running and just cranking. Don't crank for more than a few seconds, and let it sit to cool down for several minutes after each try.
When checking for spark make sure all four plugs are on the engine so there is an electrical path for every spark to the engine otherwise you will damage the igniter or the coils. With all four plugs out it will be a lot less stressful on the starter and battery.
One common issue is getting the the firing order 180 degrees out. This can happen when swapping wires or re-assembling the ignition advancer. The rotor can go on backward.
Make sure the right coil has a black wire and it fires cyl 1 and 4.
The left coil gets a green wire and fires cyl 2 and 3.
Then make sure the point of the rotor points toward the "Tec" logo when the engine is at TDC for 1 and 4.
Normally when the ignition is 180 out, nothing happens at all. But in some instances, the ignition can have a ghost spark that is also 180 out. This is a very weak spark , but could be enough to run a cylinder or two for second.
managed to get the almost running state on clip,
Is it possible for the gas to have gone bad within a month?
It's 91, octane. at this point i might pull the carbs off anyways to replace the boots, (I have new boots ready to go)
althought the fuel in the fuel filter looks fine, and flows good.
starting to think at this point it has to deal with my new harness but at the same time it works good as far as I can see. that's the biggest variable that has changed from when it was running.
Does any wire need to be larger than 18 gauge coming off the off the main harness? All the electricals work, horn, (can't really check speedo and tach atm) lights, turn signals, and was getting spark from the plugs. small detail but one of my start attempts triggered that brake failure switch somehow, so that works too.
This morning I put fresh plugs (perfect gaps) and attempted a start with full throttle, prime, choke. still only able to get the half start.
pulled the new plug after a start attempt and it looked clean still but smelt of gas. Waited a bit and gave another try and hear a low tone bubble/burble noise, kinda like a Harley that has its idle set too low.
Gonna give it a break for a couple of days.
I have spark, I'm definitely getting gas, and I don't have a compression tester but when turning the engine by hand I feel it. also the ignition is aligned properly. Outside of the battery issue, and oil burning, last month it ran great.
If you guys have any other ideas I'll try them, but might just open up the carbs and re do the top end.
I would drain the carbs, pull the fuel tank off, plug the vacuum line for the petcock, clean the plugs, and try to run on starting fluid (Ether). If it won't run on that, then it's electrical or mechanical, rather than a fuel issue.
Do you have experience running a bike on starting fluid? If not look for some videos to get an idea. You usually won't need any choke with the starting fluid, and maybe a little throttle.
If the bike runs and revs up normally with starting fluid, then the electrical is probably fine, and the engine mechanicals are good enough to at least start. So you'd then be concentrating more on fuel.