Hi all! After my massive ignition issue post, it seems that's mostly in the past for me now, thanks to all of you guys.

Before I get run over by everyone on this forum, I KNOW that this gets asked a lot, but I promise you I have done my research on the forum and off and it seems this is truly a unique issue.

TL;DR: Condenser grenaded in flywheel. Turn signals stopped working, others unknown. Relocated condenser and reconnected wires using somewhat damaged lighting coil, no lights are working. Removed flywheel and swapped damaged coil for new one, still no dice, weird voltages. 

One thing still persists, however, and this is my lighting issue. I already blew out a headlight previously and so I purchased a h4 halogen 35/35W conversion plus a bulb and it is lighting up but incredibly dim. Also the turn signals worked very recently (I noticed that at low RPMs they would just stay on and only blink at higher speeds, but I am pretty sure this is because no battery), but after my condenser grenaded in the flywheel they ceased to function. I pulled the stator and fixed the severed connections, and one lighting coil was certainly dinged up but I figured whatever shorts were present wouldn't be an issue because the wires were still continuous. After I put it all back together it still didn't work so I pulled the stator again and performed rocket surgery on it, I swapped in a new lighting coil off of an old DT1? stator and replaced it, but nothing has changed. The multimeter readings I took seem to be about the same, listed below, except I think the tail light voltage may have actually gone up somewhat the second time.

Now, on to the pictures and video. I have taken readings for the high/low beams, all are listed in the pictures. Headlight seems to be too low, but here's the kicker: The tail light is a baffling 44 volts (measured AC admittedly) and about 2.2 amps DC (my $30 multimeter can't do AC amps).
The video shows the brightness of the headlight then shows me toggling the high beam. After that I toggle the turn signals with nothing lighting up either time. 
Also included are some images of the transplant.

photos.app.goo.gl/GM7bqPCmEggZWRDF7

Please let me know if this is something any of you have experienced before, the 44v at the tail light is really throwing me. Thanks again for everyone's help, I hope to hear from you guys soon!

I''m lost [limited help] but do you think you ended up with a 12 volt headlight bulb. Bottom line is yellow from the lighting coils is your highest output so runs your headlight & instrument. Tail in US might be off the battery, but still related--or even more so if you don't have a battery. Battery [DC] runs turn signals--neutral light if fitted--horn--brake light & that's about all. So trying to run your turn signals at the moment they're trying to run off AC from [maybe green or green/red charging for the non existing battery. & there isn't enough grunt left with headlight running. Fit a battery. But headlight?? whats on the bulb. Have you by any change got a regulator fitted somewhere which will 'really' be killing the headlight if you have a 12volt bulb. Regulator [if yamaha] will just have a single yellow wire & could try unhooking under these strange circumstances you have going on. Regulator not to be confused with the rectifier under the tank--little black thing with two wires, likely white & a red i think.

Thanks for the reply as always, RT. I have just checked and it's definitely a 6v 35/35w bulb. I will check and see if there are any such regulators, it did seem to me that there was some more stuff going on in the headlight housing than just your standard electrical spaghetti, but let me know where I might look for such a thing if they're commonly found somewhere. Some plastic housings, not sure if they're connectors or fuses or what, but I'll have a look in a bit and let you know. Also, the horn and signals previously semi-worked on the AC (although I think they may receive a rectified DC power source from the AC current) but they were dim/faint at low revs, understandably. Now the signals don't work but iirc the horn does still, but it's quiet.

I'm getting out of my depth so see what others come up with. But if were me & to prove a point i think i'd unplug the mag lighting wires at the loom & try the yellow direct to the headlight, just individually to each filament wire yellow high & green low. But first a random thought, be sure black is earthing & bulb isn't trying to run both filaments at once due to no earth. Not even sure if that's possible without other things coming into play--but!!. Just be careful incase its all good & lights shine bright, so keep revs low initially incase bulb blows out. If its still very dull it can only be the lighting coil--I Think!!. been wrong before.
Could just pull the light unit out & run it down beside the bike with an earth wire to the black then play away with the mag yellow & for that matter try the others too, whatever they are, green green/red you'll know.