Did you remove the pilot/mixture screw and clean it and its respective carb orifice thoroughly? That's part of your idle circuit. If clogged, that would explain why its running only with choke. Take a look here (identified on bottom view of carb) for what part I'm talking about... https://tw200forum.com/index.php?/top...750#entry19750
The 1000 feet is not your issue. Don't be rejetting until this issue is fixed. A 2008 with 16 miles still probably had the same gas in it from when it left the showroom.