Definitely try uninstalling the wallpaper. I guess you can switch to another wallpaper and it should stop the thunderstorm one from running...however, maybe not. If it's not too much trouble, uninstall it. You might want to reboot afterwards for good measure.
Did you check the running services too?
Everything else looks OK. You don't have anything odd and you don't have any apps that require root. I might try clearing the system partition again just for the heck of it. Also, it might be a long shot but you could try a home/launcher replacement. I very much dislike the stock launcher anyway. I like GO Launcher EX, but people also like ADW and Launcher Pro. Even if it doesn't clear up the reboots, I'd check out one or more of those as it just makes life better.
Finally, if none of this works I'd guess I'd back up all of my pics and other data and factory reset