How would I diagnose where the problem is? Or do i just replace intake and exhaust gaskets? I dunno where to go from here

A leaky exhaust can be hard to diagnose. I would replace your manifolds/risers. Depending on the age of them, they may be due anyway.

Last year I had a similar problem, I took mine off, tested them with a hose, and they showed no leakage. They still leaked when I put them back on the boat. Probably something to do with the heat from the exhaust opening up a crack.

I wouldn't worry about your intake gasket. If your intake gasket was leaking, you would have milky oil, and most likely no water in cylinders.

Okay, so no water in oil, only cylinders indicates exhaust manifold/risers? Pull them off, put new ones and and new gaskets on? The boat is a 1999. I think this can be done with the boat in the water

Update: pulled the header off and it had water in the exhaust runners. So...Guess I'm closer to my problem. gasket was pretty tourched, particularly on the manifold to elbow area
Probably my leak?

Please keep the help coming, I'm working live on it. Everybody's help is getting me through this one!

replaced manifold and riser gaskets, problem still exists.
runs great once started, water must be running in there when the motor is off

you could have another problem also. i would first check your thermostat. it should be a 160 degree stat. the next thing is if the water temp is erratic it could be the circ pump and what could be happening is it is not circulating and just relying on the raw water pump to move the water. also if the temp is going up and down the ecm see's a hot cold situation and constantly adjust's the fuel and timing curve and idle air control valve to kepp the engine running. you might also have fouled some spark plugs due to this condition all causing you rough running condition. you are also going to wanna check the exhaust flappers in the y-pipe chances are you burned them up. run through all of you coolers to check for impeller debris if you broke off any veins. they can make it up to the t-stat and get stuck in it and hold open the stat enough to allow water to flow to a certain degree but not enought to get the engine hot enough to open the stat fully open.

If your flaps are good, Replace manifolds and risers. They can crack, or have other problems, especially at their age.

You are seriously playing with fire here, I would almost guarantee that your valve sealing has been compromised at the minimum at this point. The water in the cylinders is not exactly clean, and the valves are closing on it.

I learned this the hard way.

B.O.A.T. stands for "Break Out Another Thousand"

I dunno if you said, but what is compression test numbers? Rough running soundslike you hurt a valve , but a compression test would show that. Do all 8 cylinders and look for good correlation between them. I over heated a SMC (Volvo Penta but same deal) about 2yrs ago by hitting a plastic bag and shut water off while cruising about 3500 RPMs. Got WAY hot, motor shut off, water boiling everywhere in engine manifolds, melted all the exhaust bellows (lower "Y" pipe is under waterline, boat almost sank, ...sweet design there huh). Anyhow. Got it running and immediately filed cylinders with water. Did a compression test and it showed OK, weird. Turned out torched both riser gaskets. Was due for them anyhow so I replaced both manifolds and risers. Did a total tune up and lots of oil changes and I have put about 300 more hrs on motor. Moral is sometimes you get lucky, don't give up yet.

I'm ruling out exhaust system as the problem, when I had the manifolds and risers off there was still water coming in the cylinder after cranking it over. Must be the head or intake gasket, guess the top end is coming off.