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I was going through the jetting procedure. The engine would stop with the air screw in. Also, the engine was running with the air screw one turn out. I decided to reduce the pilot jet. Then I warmed up the bike with quick lap around the neighborhood. I get back and start to adjust the air screw. I was moving the screw trying to figure out the best adjustment. I wasn't happy and turned the screw all the way in. The engine kept running. Ok, I swapped back to the original pilot jet. It started, but now runs with the air screw in all the way.

Original pilot jet 48
New pilot jet 45

Any thoughts?

Literally, it doesn't matter one bit what it does when fully closed. Always start at least 1 full turn out and keep turning out to where you get your highest idle speed. Ideally, around 1.5 turns out on the air MIX screw to know if you have the correct pj. However, it can be 1.25 to 1.75 turns out and be good. Anyway, more than 1.75 turns = need a smaller pj, less than 1.25 turns = need a larger pj. Always adjust the idle mix after the bike is fully warm.

Also, make sure you don't have the idle SPEED screw (not idle mix screw!) screwed in too far causing you to also be on the main jet/needle a bit as it makes getting the correct pj impossible.