Throttle should be smooth no matter what ECM you have as long as it is a good fuel map.
Geometry didn't change with comparable bikes in the XB line their entire run (except Uly's weird fork stuff). I would assume the front tire is worn on the '09. Even with tread left, they HATE being V'd out and will 'fall' into a corner where you need to catch it. So it act like you push the bars slightly, it turns in too fast (yikes!) then you have to adjust the bars to keep the same lean angle. I hate that and all of my Buell XB's wear fronts like that, especially with cheap tires.
Try swapping front wheel assemblies between bikes, heck.. might as well do both ends, and see if that livens up the '09.