Did that jet kit recommend a bigger pilot jet? Sounds like that is where you are running lean. Try a # 40 pilot jet and I'll bet your problem will go away. When I was running my stock carb I used a speedstar kit and it required a change in the pilot jet. I used a # 45 and I used a 180 main jet with the needle on the 4th groove and it run great. It is not the same as when jetting with a Barons kit. BTW
+1 on this.
The carbs have an overlap between the circuits(primary, midrange, main)
In that idle to 1/4 throttle, your not getting the fuel up through the pilot circuit that you need. The carb is drawing fuel primarily by vacuum at this point, because the throttle plate at the back of the carb, is mostly closed.
When you get past the 1/4 point, and the plate opens up enough for the carb to convert to the venturi action to provide fuel for the motor, your pulling fuel up through the main circuit. When your not relying on the pilot jet for fuel anymore, then your bike runs better.
However, due to the overlap, and the fact that at a normal cruise, the bike doesn't have alot of throttle( right at about a 1/4 throttle), it reverts to trying to pull fuel from the pilot, and it isn't getting enough. Therefore, your seeing the lean indicator on your pipes.
You'll get some more ideas. It's a big weekend, and lots of folks are away from their computers. The pilot jet's an easy fix, and can be done with the carb on the bike.