Well I see you live in texas where your winter weather is probably as warm as our summer weather minus the humidity. You say you use 50% choke. I cannot use it at all and it's only 25 oustide, ok maybe maximum of 30 degrees celsius which should be around 90 Fahrenheit. If I do the bike stalls. Can the TPS adjustment affect the choke? I would doubt it.
About the hesitation now...it does go away when warm but I am wondering if it's a knock because not enough oil gets to the bearing or backfire because of the lean condition? I am inclined to say it's a backfire since the RPM go down a bit, if it was a knock because oil starvation I don;t think it would have an impact on engine speed.
Throttle response seems good but I sometimes feel the bike should be faster, at least it felt faster when I got it ( I had a KLR
). It felt a bit slower after the valve adjustment but it';s either I got used to it or the acceleration was more linear after valve adjustment.
Gas mnileage is not that great at 36MPG but that might change since I had that result while breaking it in and varying the speed a lot with roll-on.
What mileage do you get? Is the bike stock or did you fiddle with the carbs and exhaust?