I have a Honda cbr600 2009. The battery was running low so I went to recharge it but accidentally switched the poles. There was some smoke and a few sparks from the battery after about a minute. Once I realized what happened I took them off everything was hot. I let it cool off for a few hours then corrected the charge. surprisingly now its fully charged and I haven't noticed any fuses blown and under glow lights connected directly to the battery are working. Except nothing happens when I turn the key.
With luck, all you've blown is the main fuse.
Check all of your fuses. Apart from the fuse-box, there may be a separate fusible link somewhere. If they're fine, or you sill have the problem after replacing any blown fuses, get the bike transported to a Honda dealer. There's no telling how many electrical components are fried, but they can figure it out by substituting known good components for the ones on your bike. This is the kind of problem that will likely leave you chasing your tail forever if you try to diagnose it yourself--and you might end up wasting a LOT of money on components that didn't need to be changed at all. Remember, there are NO returns or refunds on electrical parts. Chances are, you're in for a BIG repair bill--what you did is catastrophic.
You ruined your stator I bet.
If the key was on during shorted time you may have fried the ignition system.
