Chapter 1
First things first. Do as the wise man Monte (who's admittedly been in your shoes) says:
Have a beer, then disconnect the batt's neg cable, remove the front cover and check for a scorched spot on the diode board.
If you find a burned looking spot and smell that sad, burned electronics smell, well... eBay is your friend.
I might add that Rick Jones at motoelekt.com also stocks diode boards and is a pleasure to deal with.
There is no main fuse on the airhead's electrical system. If I sound like a parrot on Monte's shoulder, it's for good reason. As he said, you probably zapped the diode board when you juiced the system with reversed polarity. It's an easy check and nothing will work if it is fried. Just make sure to disconnect the negative lead on the battery before you remove that front cover. If the diode board is still good, you could wreck it by shorting it out.
Though the airhead electrical system has it's flaws (no charging with a burnt-out gen light, crappy bosch stock coil, no good charging until midrange rpm, troublesome--for some people--ceramic strip fuses), it is pretty simple and straightforward, like the rest of your bike. No need to rewire the thing unless it's been hacked apart or burned up by the battery mishap.
Chapter 2
The stock ignition system should be able to start your bike at 40F. If you have hard starting issues, there are a few things to address. 1) The battery must be in good condition 2) the enrichener "jets" in the corner of the carb bowls need to be clear, as do the holes in the enrichener discs. 3) the plugs should be correct, gapped correctly, and not fouled or worn out. 4) the plug wires should be good. If in doubt, or if they are original, they should be replaced. 5) the coil should be good. The stock grey-colored bosch coil is notorious for cracking. It can still work once cracked, but poorly. 6) the valves should be checked/adjusted and the carburetors tuned.
Starting fluid is ok to use, but think of it as a band-aid... don't use it on a broken bone. The reason it is popular with (big) diesels is that they don't all have glow plugs or manifold heaters. They just crank em until they start. Starting fluid is actually worse for a diesel than a gasoline engine. Diesels have no throttle (only an accelerator) and rely on the injectors for "ignition" timing. Putting starting fluid in a diesel puts it at great risk of detonation, as the combustion chamber develops enough heat through compression to ignite fuel in the cylinder, whereas a gasoline engine needs a spark to ignite the (starting)fuel/air mixture.