I'm considering adding water thermostats to bring the temp. of the motor up to 140 degrees. The motors currently run below 100 degrees. Do I need to install some kind of bypass in case the thermostats get clogged?

You have to have a bypass water nek to run water to the exuast at all times. You also need a circ pump to run a T-stat. If you call Rex marine they have complete poppet valve kits that work well if you don't have a circ pump.