Is it a TBI 350, or LT-1 350? TBI motor (truck motor) had iron block and heads, you'd have to be over 230 before worrying about the tmep ruining something (unless you're running at that temp for a long time).
LT-1 engine has aluminum heads and over 200 is dangerous. The LT-1 has a retard mode that kicks in around 180 (I think) and limits the engine to under 2000 rpms. Thats probably the running rough you feel when the motor is hotter than normal.
If you're normally at 140 operating temp, then you have the wrong top t stat.
When I said 200, that's the static temp of the hot engine sitting without cooling water circulating. That goes down immediately upon starting back up.
Check the Mastercraft website, www.tmcowners.com
there is alot of info there and also on the old MC Forum (can access from the main MC Boat website under classifieds.