Not sure you're looking at the tranny cooler on that boat. The cooler is inline with the 1 1/4" raw water intake hose before the raw water pump itself, and not on the transmission. You should be able to pull both water hoses (not the smaller transmission lines) and look straight through the brass cooler tubes to check for debris. Flush with a garden hose and/or use a piece of wire to clean out any lake garbage. Usually ends up being a good bit of junk and hard to miss.
Your problem does seem to be an obstruction somewhere (likely before the raw water pump) versus damaged raw water pump vanes, but check for those anyway as it being starved for water will cause them to deteriorate fast. If the intake is clear, keep tracing the path throughout the motor. May help to used one of those infrared temp sensors from Lowe's or HD to detect hot spots if you need to find a blockage in the motor cooling path (ex. headers running cool but motor hot), but hopefully you find it on the intake side of the raw water pump.
Last edited by 93ProStar205; 06-15-2013 at 10:12 AM.