Sounds like a few gremlins to me. I tore apart my whole loom like that.
FIRST, I would check fuses. Then I would check behind the headlight... it MIGHT be a mess in there. Earthed out. Often if you dont have voltage, the brake will make the tail light dim a bit.
It could be a poor earth also poor connections.
Will take time to sort unless you get lucky.
With the bike off, just the wiring, trace the tail light wire and the brake light wire to the switch (brake switch) then, take them both (positive wire) and connect it DIRECTLY to the fully charged battery positive terminal. Does the light do the same thing? ie, put the tail light wire on first, then while holding it there, put the brake light wire on the positive. This will tell you if its in the wiring... if its perfect, then look at the brake light switch, could be poor earth or poor connections.
Headlight could be as simple as blown globe. Could be the headlight switches on the bars.
Again, I would personally open up healight, connect neg to neg on batery and pos onto pos on battery... if it works, its not the light. I would then trace back.
First thing I would check though is the earths... tail light/brake light and the headlight.
I have seen in the headlight chopped wires, hacks, etc and they short out causing all sorts of issues.
As for charging, thats a whole other issue. Alt bushes or other...
Reminds me so much of my 81... which now has only about 3 wires total