First off, you were right about the 09 pilot jet being the same size as the 07. They were both 42's. When I looked through each one they looked the same and had the same size hole so my theory on the other being jacked was off I guess. I put the newer pilot jet in the 07 bike and got the same result.
Let me try to further explain the problem with a little more detail.
The bike starts fine, as if it were going to run perfect. 1st or 2nd kick and it idles perfect.....even off of choke. When I start to rev it OFF of choke it starts to rev and then sounds like it's running out of gas because it starts to sputter and will die unless I let it idle again and then it will idle just fine. Same thing, rev it up and it appears to run out of gas unless I go back to idle.
The weird part is that I can rev it ON choke and while it doesn't run perfect, it does in fact rev up like normal.
My question is; is there some other control that feeds the carb when the throttle is engaged off of choke? Could it be an air fuel mixture that is really off and causing it to mix wrong when the throttle is engaged? I'm wondering if maybe I put the long needle jet in wrong....maybe that's jacking with it. I made sure the main jet is not clogged and the pilot jet is pretty much new. The air screw is turned out 2 and 1/4 turns out.