Two prong is OK.
X is the hot
L goes to T/S switch
If you had a third, it would be P, which is Pilot, which is either a indicator light on the switch or dash. You can tap into L for this. L is the blink signal.
You can see the X, L , P on Gdads51 diagram of Grote.
"I’m sure there was a short somewhere as while driving I’d see a bright light flashing in the controller as though it was blinking."
Seems like the only place to "see" inside the switch is the indicator window, so it was probably blinking. Was the hazard accidentally on? Jiggle the lever next time to see if it stops.
Are all your bulbs incandescent? No LED? Next time it happens, pull over and see if any lights are flashing, front or rear.
If you add one more problem to this deal you will win a Trophy and a free vacation to Mogadishue, Somalia. Bring a sweater.