hm
I had a Quadsport 230 that did that after I didnt put a part back on at the point where the muffler goes into the motor. I forget what it was but I remember thinking it unimportant.
It would run till she got hot, then it would start to sputter and stall. It would take about 15-20 minutes befor she would restart. It took a week of trying all the above stuff before I decided to put that small part back on it.
It ran great till I sold her a few years later.
Just a thought in case you messed with the exhaust and its missing a gasket or whatever.
84-85 Custom Tecate
1986 Honda 200X Daily Rider
2006 Suzuki King Quad