03′ 350 TRX Carb Issue?

Hello all! I have been coming here for years and have found a lot of great information and for that I would like to say Thank You! I have an 03 350 TRX 4×4 atv I bought about a year ago. When I bought it it had a decent amount of white smoke when riding (decent enough to where I knew it would need the top end rebuilt at some point). I recently opened it up and had the cylinder head bored and honed and new piston with new rings, valve seals, etc. I also, while I had it apart, rebuilt the carb and replaced all vacuum and fuel lines. I put everything back together (I followed specs in the owners manual on pretty much everything). On the stock setting for the pilot jet, the quad started and ran great. No smoke, no sputtering, didn’t seem too rich. It was actually running about perfect. I knew that to set the pilot jet it needed to get to temp, so I let it warm up. While setting the jet, the engine would be at a decent idle and then it would click (sounds kind of like a shift of gears), and stall. When it would stall it sounded like something was still spinning in the engine and winding down. I can adjust the idle screw to a higher rpm to temp avoid the stall, but am concerned about it. Also, when the engine is at max rpm, it almost sounds like it is missing a bit (like a hollow sound). It doesn’t sound in sync to me. I am suspecting my pilot jet might be the issue, but wanted to reach out to you all before I pulled anything else apart. Any thoughts would be greatly appreciated!