Yes, leaving one plug wire unhooked can short out the coil. It may or may not have hurt your coil.
On my green coil I get a 25.1K reading on my meter on the 200K scale from one cap to the other. Put the test probes in where the caps goes on the spark plugs. If you remove the caps and check from the end of one wire to the end of the other it should read 15K. If you check from one cap to ground you should read infinity.
The primary side, 3.3 ohms.
If it ohms out to these specs it should be ok.
The rain shouldn't hurt anything. If any of your wiring wasn't covered well enough it could have gotten wet enough to short power to ground and make it quit. Mine used to. Once I got it wrapped up good so water couldn't get in, it runs fine in the rain.
You might want to check the voltages at the coil and Pamco. If you aren't getting battery voltage there you won't get spark.