Your answer is in the previous posts.
Originally you said it happened while trolling, suggesting impeller,plate, etc.
1. Extend the hose right where input hooks into the motor. (thermostat housing) Start it cold and run for 15 seconds at the correct rpm to see if you have enough water coming in.
2. You can also put a clear hose from the cooler to the thermostat housing to check for air bubbles. Air bubbles means restriction.
You said you ran it without thermostat and still had problem that sounds like a water coming in problem, but maybe not.
3. If you have good water flow, then pull the rubber boot and see if a flapper broke and is plugging water going out.
4. Pull the elbow off the exhaust and check for rust. Tap it on a board to see if anything comes out. If you've got blockage here, you probably have blocked passages from the manifold,spacers if you've got them, and the elbows.
There is a service bulletin from merc for the gaskets-make sure you put the right ones in. You haven't said how long you've had the boat, if it's been in salt water or not. If someone replaced the manifolds before and put the wrong gaskets in it, you need to know if you have the restrictor or free flow gasket.
If you suspect the exhaust, before you go any further I'd call Hank and have him LOOK at it.