Do you have a multimeter and a wire diagram for your bike? Almost a requirement for isolating electrical issues. And, certainly data from measurements will help in an on line dialog.
The stock flasher unit is sensitive to the bulb resistance and is tuned for the ones installed stock. What wattage bulbs did you install at the flasher positions?
The green wire near the flasher unit is a ground that three prong flashers need to operate correctly. with your modification, you may need a flasher unit that is three prong and not load of voltage level sensitive.
Also, never assume the frame ground is a proper return path to the battery, Honda relied on the solid green wires to provide that function. All lighting should have a power delivery wire and a return green wire connection.
The wires behind the rectifier include a green wire that is bundled, and terminates to frame ground up near the coils. The entire length of wire in that bundle can overheat and melt, not only its own insulation, but that of other wires in the bundle, too. Many odd electrical things can occur when wires in that bundle cross connect. I had a 76CB550F that this happened to. I unwrapped the bundle and replaced each of the damaged wires.
I was thinking that maybe at that rpm the grenerator melted some wires in the bundle of wires behind the rectifier, (the rectifier was quite warm) and thats why my tail light an brake light dont work.
While the alternator has the power to melt wire insulation, it will only do so when other faults are present.
Any thoughts on this before i just run new wires for things?
Adding more wires won't correct the faults unless you bypass each and every fault in the existing wiring. Are you prepared to make a new wire harness?
Cheers,