I've experienced sudden engine shutdown after about 30 mins of riding through the city (Stop lights and stop signs are frequently encountered). I then attempt to electric start it and it acts like the battery is dead. I roll start it from 1st to 2nd and it sputters and shuts down again. I've noticed that this happens once the engine gets warm/hot. I've also noticed that my fan doesn't turn on anymore like it used to since my lowside in the Tahoe/Reno Mountains. Are these signs of engine overheating and an electrical protection, preventing heat damage to the engine? Like I said the fan no longer turns on and I can't remember the last time I had a coolant flush/replacement. I've gone through 2 batteries - 1 of which is brand spanking new!

If overheating isn't the cause could anyone describe what they've experienced with engine shut down and the cause? Also I think my CCTL is gone because the tapping sound matches the throttle blips and goes away @ a higher RPM and higher Speed (The sound is noticable right @ engine start but quiets down after a bit of a warm up)

 

The temp gauge should be a telltale sign if the bike is overheating. As for it just cutting out, there are a handful of electrical points that could cause that. The problem sounds electrical. There are a few switches that would cause the bike to die. The one that comes to mind after hearing of a lowside would be the kickstand switch. Best bet would be to pull out a manual and a multimeter and just work through what sounds most logical and work backwards.