I do have that problem. It is a pain in the a.. In fact, it is so annoying to have the engine shut down every time I hit the brakes when it has reached operating temperature, that I am buying a new engine.
Tuning this engine is very, very cumbersome; said by me, said by my LHS (which sells a lot of CENs). There is no way you can set this engine up to have more than 2 laps in a track without it shutting down.
If you manage to do set it right, let me know but I truly wish you luck.
I am just buying a .30 or .32 engine; Andrew Smolnik, CENs racer, uses a .28 anyway and kicks butt.