[shorod]

If you're measuring a low resistance path to ground on both fuse terminals, with the fuse removed, that definitely would suggest there's still something wrong in another circuit besides the one that the fuse was pulled for. If all other fuses were out and the hot/supply side of the fuse was measuring low resistance to ground, then the issue would be somewhere between the battery positive terminal and the fuse. A higher resistance would be less of a short, so the primary concern would be a circuit that measures less resistance to ground.

According to the wiring diagram for the flasher circuit, there appears to be an 8-pin DIP integrated circuit (IC) that controls the turn signal flashing and hazard flashing. That block diagram shows a PNP bi-polar junction transistor (BJT) driver for the relay, and the collector of that BJT is tied directly to battery power via the 15 amp fuse when the ignition is on (or through the Horn fuse if the Hazards are active). There's a pretty good chance that BJT or other components within the IC blew from the reverse polarity.

Do you have access to the turn signal flasher to confirm you have battery voltage to terminal B, ground at terminal E, and a pulsed signal at terminal L when the ignition is in the Run position? You most likely have some power to terminal B and a ground to terminal E since the flasher is clicking. Since the hazard switch does nothing though it would seem you're never getting a pulsed signal to terminal L. Are you saying that at least some indicators on the LHS still work?

Regarding your alternator, I hope you measured more like 30 mVAC of ripple. 30 VAC of ripple, when rectified, would still be around 21 VDC (RMS) which would be dangerously high for the 12V charging system of your car.