please help - freaking out.....

.....alright here's the story:

I have 2000 Inruder 1500 LC

Put new pipes on the bike - all fine - but battery was low.

SO I quick-charged it and took the now awesome sounding bike for a spin...so far so good....then I made the big mistake of stopping at a parking lot to grab a smoke.

When trying to start the bike back up - no go. OK, I figure - battery ran out of juice...(since I had been starting it over and over to fix some issues with pipes, etc.).

Ok, no biggie, call my girlfriend to bring over some jumper cables - ok hooked the jumper cables, all the sudden sparks fly and the bike won't even turn on!
Meaning: turning the key = no lights coming on whatsoever.....

Well, crap, have it towed - check the battery, battery seems to be fine...charges and everything.....reinstall it, and STILL no lights coming on.

I checked the fuses but can't find anything wrong....and now I fear I might have fried something more vital then just blowing a fuse.

Any suggestions? I'm in dire need!!!!!