I think I have a corsa exhaust system. My through hull exhaust only has a flap that closes off the main opening and diverts the water and exhaust around that flap out the same exhaust pipe. I have heard that you should not run your motors above 3500 rpm with the silent exhaust on. Is this the case with my setup? My exhaust does not go down through the drive unit, it just goes around the flap and out the transom.

It depends on the engine and the cam that you are running. On cams with a lot of overlap, reversion is the big worry with restrictive exhaust and water that is mixed into the exhaust stream closer to the cylinders, but that is mainly a factor at low (idle) speeds. Almost all Merc black engines (non Mercury Racing Blue motors), you would be just fine to run it at any speed you want with the exhaust closed, even running it thru-prop is not an issue with these engines, as the cam timing is quite mild. I have seen many 454 Mag powered boats that do not have transom exhaust, and they are just fine.