Perhaps I'm an optimist, but I wouldn't start yanking wires out just yet. I still haven't heard anything that says to me your harness is hopeless; and replacing the harness isn't going to fix bad switches, or bad lamps, or bad connections (well, not all of them anyway).
You are quite correct, the turn signals should work independant of the light switch even being connected; except of course that the lamps still have to be grounded.
But first, I would concentrate on why you are seeing "major discharge" with only the ignition switch on. The ignition coil should only draw about 3 amps, which is only a small deflection on the ammeter. And with the turn signal switch in the center position, there shouldn't be any turn lamps on, including the yellow lamp on the dash.
So, be sure everything is turned off, and pull the hot wire off the coil. If you still see deflection on the ammeter, start hunting for where the power is going. Pop the fuses out of their holders (although only the one with the extra terminal next to it gets it's power from the ignition switch). If you still see a discharge, check all the lights then start feeling around for what is getting hot. The red light on the dash should be on, but it won't draw enough current to even see on the ammeter (around 1/6 amp as I recall).
Once that is solved, then focus on why the yellow lamp is on. It's normal for it to glow just a bit from the light from the red lamp (the colored plastic extends behind the dash so one shines into the other to some extent); but it should not be on brightly with the turn switch off. If it is, most likely the flasher is wrong, defective, or mis-wired.
BTW, when I checked at the local parts stores, none of them had a proper flasher for the TR3 even though they claimed it would work. Their "universal" 3-prong flashers just don't work right with the stock TR3 wiring. A Tridon EL-13 "electronic" flasher was the only one I found that worked right. Eventually I rewired the yellow light so it would work right with the generic 3-terminal flasher, but the stock wiring won't.