But I gotta say, the bike did feel more flickable without the 5lbs battery, it's probably not so much that it's 5lbs, but that it's a the top of the bike, raising the center of gravity.
This is why I found the Ebatt, 08 YZ exhaust to be such a crucial mod. With 5-6lbs of high weight removed the bike is much more flickable
I'm surprised you're bike ran without the battery. When I first put in my Ebatt I didn't have it connected to the stock charging system, and when my battery went dead my bike would start but not run. It would just pop and misfire with any throttle. It was my impression that the CDI would not work properly without the battery on 07's and later models