2013 Maverick random engine stalls.

I am a new member and needing a little impute on an random engine shut down problem. It all started when I overheated my machine, due to. coolant bleeders leaked at about 2000 miles. The reservoir is very hard to see coolant level, my mistake and low coolant, hot day, equals overheated system and goes into limp mode. Since then I have been experiencing a random engine shut down. I found cracked spark plug boots, replaced them with new factory boots (double zip tied the boots). I mounted a external fuel pressure gauge and fuel was not a problem. Went through electrical connections, battery voltage and all grounds. I am currently at over 5000 miles and still researching a solution, local dealer mechanic out of suggestions. The engine will shut down, I turn off key and back on again and engine starts till the next shut down, 20-200 miles later. Usually not a problem, except riders coming up behind me. I am now designated rear position rider. I bought the machine a year ago from last May, crate machine (lost in inventory). I have ordered new wires and boot ends from MSD.