I've been warned that a trans flush on an older transmission could cause problems. Does the same hold true for a coolant flush and fill.? Is it possible this process would loosen built up gunk and clog the system.? Specifically I'm thinking it might cause a problem with the thermostat. Any help would be appreciated.

You should change the thermostat with every flush and refill. Which year is your truck? If it is a first gen with the V6 it is very easy to swap the thermostat.