2003 buell xb9 running poorly at idle bogging out at 3000rpm when given throttle and sometimes backfiring out of the intake. I have had to jump the battery a couple times in the recent past.

First, any modifications? running an aftermarket pipe or open intake without changing to either a "race ecm" or getting the original re-programmed via ECMspy or a similar software package can result in those issues.

If that is not the case it sounds like a vacuum leak. and I've heard of a few people having to replace the seals underneath the throttle body. check this out by spraying a bit of carb cleaner down around that area and if the bike picks up idle then you've found it.