I have a 97 gen 6 496 custom built engine that has been in storage for 18 months and now has an overheating problem. The engine was running fine before storage. The engine was fogged and filled with -50 rv antifreeze along with all filters and fluids changed. I ran the engine on a hose prior to dropping it the lake with no problems. I ran the boat from the launch for about 2 miles to my dock with no issues. Picked up a few buddies and cruised for about 5 miles and then entered the no wake zone and pegged the temp gauge to 280. I made it to a marina gas dock without the engine dying. The left side exhaust flapper was almost white from the heat.
This is the setup I have: DWP Bravo XR flowing water to Hardin sea strainer.
1.25" hose from strainer to dual stage water pump. One stage to intercooler and the other to engine.
1.25" hose from pump to Hardin oil cooler.
1.25" hose to Procharger crossover w/o thermostat.
I have changed both impellers in the pump. They showed signs of wear but were not that bad.
I have backflushed the system from the engine back.
I have drained the block 4 times. There was some rusty water found. I filled the block with a hose at the drain points to stir any more sediment up and drain it out.
I removed the headers and drained them out. Nothing was found in them.
I ran the engine on a hose from well water so cold it made the water pump and oil cooler sweat. Engine still overheats.

The engine starts and seems to run ok on the hose but the temps slowly rise and just keep climbing. The exhaust does not seems to be flowing enough water through the tailpipes and steams a lot when the temps start to rise. The headers are very hot to the touch. The oil looks perfect. No milkshake.

The engine is a Procharged R-tech intercooled 496 with AFR 315 heads making over 800 hp at 8.5 psi with 88 hours on it.

So what was the soution? Having same issue

Did you change thermostat?

Just pulled two stones out of lwp. Would cool fine up to about ten mph.

Some days are diamonds and others are stones

all the best

3pointstar

Pull the water hoses off from the raw water intake to the last and see if there is any water pressure issues at each component. Check sea strainer and components for air leaks. Just some thoughts.