Hi Bill, sounds like you have your hands full! I will focus on the idea that your problem could be cooling water related.
You said it is fresh water cooled. I want to make sure we understand what you mean by that. There are basically two ways of cooling a boat engine. The first is the water you are floating in (lets call that "sea water" for now) actually circulates right through the engine block. The other is the boat engine has a closed cooling system like a car does, but instead of a radiator a boat uses a water-to-water heat exchanger to get rid of engine heat. The engine coolant flows through one side of that heat exchanger, and "sea water" flows through the other side. That second system is sometimes referred to as "fresh water cooled". Fresh water cooled boats have two water pumps -- one on the engine (like a car) that circulates the engine coolant through the closed system, and one to pump the "sea water" through the other side of the system.
Assuming that your problem is cooling related, and knowing that you have replaced the thermostat and pump impeller (I'm assuming that is the impeller on the "sea water" pump), it is possible you have a blockage in your cooling system somewhere. You mentioned that the pump was bone dry (again assuming your are talking about the "sea water" pump). That makes me think you have a blockage on the sea water side. Make sure your thru-hull seawater valve is open (obvious, but never hurts to ask). If that is open, you will want to check the flow in your sea water side to make sure it is free. Old pump impeller rubber parts can get stuck in places that will block the flow -- next time you have your sea water pump open, take a dental pick or something similar and probe both the intake and discharge sides for any rubber parts.
Something we did to find our overheating problems was to take the tubing apart where the "sea water" goes into the engine exhaust risers (we checked to make sure that tubing was above the waterline so we wouldn't flood the boat), and then fired the engine and timed how long it took to fill a 5 gallon bucket. Did the same on both engines, and found the seawater system on one engine was only putting out about 1/2 the volume as the other side. We backflushed the seawater system, took the heads off the heat exchanger, and did other things until we found our problem, which was old impeller rubber crumbs in the intake elbow of the pump (how did they get into the intake side of the pump instead of the discharge side -- who knows?).
On the 427s there is also a spring loaded "relief" popit valve where the seawater goes into the exhaust risers -- that can get crudded up and taking it apart and cleaning it up will be helpful.
One thing you NEED to do is spend $40 on a Digital Non-Contact Temperature Gun (you just aim it at what you want to read the temp of and pull the trigger - and the temperature will be displayed). If you have a temperature problem, that tool is critical for finding it. Constantly check the temps off all parts of both engines, and if something is overheating you will find it with that.
I don't remember you saying what boat you have -- maybe I misse it. Let us know just out of curiosity.
