WTF is wrong with my bike now?!?

So after replacing my battery a SECOND time (bike worked fine for a month, then it would sporadically not start on me...but only if I'd already been out riding and had turned it on/off a few times running errands or whatnot), my mechanic thought we had a fix and the issue was just a bad battery. I ride an '03 R6, btw...

Well, everything seemed fine for a bit, charging system seems good, bike turns over the first time, every time, idles around 900-1100 rpm typically, and so on.

Now, however, it seems that when I ride long enough to warm the bike up sufficiently (like 15 minutes +), if I make a stop and turn it off, then start her up again before she cools down (i.e. sits for a few hours) she idles real low...around 500rpm, maybe even less...sometimes kinda bouncing between 300-600, sometimes just hovering around 500. She doesn't die completely, but I've been afraid that she might on several occassions. I cannot for the life of me figure out wtf is going on with this damn bike, and why she is treating me like this after everything I've done for her. Aside from cosmetic upgrades, all she has is a Micron slip-on and braided lines, so I can't imagine it's anything related to performance upgrades. I feel like she really is a woman, complete with mood swings and PMS. I've become so annoyed that I'm thinking about selling/trading her for a Honda as I never had any issues with my previous one...but she's so f'ing sexy that I don't want to let her go.

Please, someone help...I don't want to break up with her, but I'm afraid I might not have any choice if I have to keep living like this.