Here's a post I did on Malibucrew when I was fighting through this on a 2012 Indmar. Some of this is down right basic, some is more convoluted. Some is specific to Indmar. But maybe there's something in here that will help as well.
I've been fighting a cooling issue for the last three years on my 6.0 and thought I'd share a list of literally everything I went through that helped to solve the problem. This goes from incredibly trivial stuff to the more interesting. Most of the information was pulled from different threads on here so THANKS to everyone over the last three years that provided assistance.
And don't give up. In my case I had three separate problems that all contributed to my issue so when I found one and thought I was good to go I got frustrated that the problem didn't go away.
Make sure the raw intake valve is completely open.
Make sure all hose clamps are tight. Probably easiest to just trace from the raw water intake through the entire system and check for loose hose clamps along the way.
Make sure the transmission cooler screen is clean.
Make sure the impeller is good.
Make sure the shaft seal is NOT plumbed into the transmission cooler. Mine was plumbed in wrong here. On an L96 the transmission cooler is on the vacuum side of the cooling system so if the shaft seal is plumbed into the transmission cooler you’ll suck air. If it is plumbed into the transmission cooler you can get a brass plug to screw into the transmission cooler and a T from your dealer to plumb the shaft seal into the correct place.
Make sure the vent line to transom is clean. On the transom you’ll see a little metal port about the size of a button on your jeans. After running the engine and shutting down it will continue to vent water like its peeing for a few minutes. If it isn’t venting water it’s plugged up. There’s a hose that will run to the top of the engine. Take that hose off and blow it out with compressed air. Mine was plugged up.
If you have a heater make sure the heater circulating pump is running. You will get heat even if it isn’t running so don’t make any assumptions based solely on if you have heat. If it isn’t running first check the fuse for it. I had an inline fuse, which was blown. If you don’t have an inline fuse Peter from Smooth Water Sports has said it will use the Fuel Pump #2 fuse in the fuse block on top of the engine. If the fuse is good the pump itself may be bad. I had both a blown fuse and a bad pump.
Make sure the thermostat is good.
Make sure the temp sensor is good. Hopefully someone else can chime in on an easy way to test it.
Check your engine serial number. Indmar published Service Bulletin SB2012-3IN to address a cooling issue with the L96 motor. It affects 2012 and 2013 L96 (6.0) and LS3 (6.2) engines with tube and tube exhaust manifolds and 7-digit serial numbers before serial number 2249300.