What is the best method of breaking in a new bottom end on a lt250r s stroke quad, I have been told to startit and let it idle for 5 -10 minutes, then let it cool down, do that 3-4 times and then ride it normal.

 

yes, also don't go past 3/4 throttle for about 50 miles, and don't keep the throttle pinned in the same position for long periods of time.
They key to a long lasting engine is to keep it rich until it is definatley broke in, and the most important thing is to let it warm up good before each ride!!!!!!
I have lost a few motors due to these cold-thrusts.