Ok...I have a 27 cougar cat...it has a 496 ho....the pick up is in the right sponson .... It has a whipple on it and runs great except for one thing...at higher rpm. About 4000-4200...the temp goes over the set 180...
if I slow down it will drop to 170-174....I can run 3800 all day...temp sits at 170-180...
I have stainless harden pump..new thermostat...cleaned exchange, new gaskets..at idle temp goes to 150....
I am lost.

I would check water pressure thru out the whole RPM ranges.

Next possible answer aerating water flow into the engine ? One can use the clear hose method for testing to see how much air / air bubbles / air pockets is being induced into the cooling side of the engine.

Next test water flow volume output test after the sea pump.

Are you by passing too much water volume ?

Stock heat exchanger? Running Whipple's 120* thermostat? Be careful running in boost at those temps. Whipple states no boost if temps are over 160*. Gauge accuracy compared to scantool?

I assume this is a new problem and it ran cooler before? Does your water pickup feed entire water system or just the Whipple intercooler?

BUP's suggestion on water flow testing is spot on to isolate the problem.

It ran boat hotter than I thought it should before the whipple...I am running stock heat exchanger...I have been very careful running it..not pushing engine just trying to dial it in...temp gauge matches the tech mate reading...looking at adding new transom pick up and sea strainer for just the engine and separate pick up for whipple intercooler....

I think this would be be paramount. Can you use your outdrive pickup(s) plumbed to the intercooler?

That's a good idea....right now I am not even sure where the outdrive pick up goes...I know it's not going into sea pump...

Are you running the Whipple 120* thermostat? What temps before the Whipple? Feeding your setup from the outdrive water pickups should be the correct way. Some just feed the Whipple intercooler only from a transom mounted pickup. The intercooler works to well if fed water all the time from the drive pickups. Mostly noticeable running in colder water. The fuel would actually not atomize and puddle in the intake floor.

Yes it's got the 120 thermostat...temps before whipple...180-185 before it was on to...but the computer is now programmed to 180 at 4k rpm..before alarm world not sound till 190...it's been really confusing trying to get this to cool off