I have a 1996 35 lightning. My right motor started running hot after 15 minutes, pulled the sea pump off and notice the sea pump housing cracked and rubber piece inside was trashed. flushed motor and put new sea pump on. The problem is i can only get water spraying out the exhaust when its running while the gate valve is closed and under pressure. If i open the gate valve and put the boat in the water without the pressure from hose it will not spray out the exhaust when running.

The question is did you get all the rubber pieces out? sounds like you are blocked somewhere, Flush again.
Rich

If you trashed the impeller, Back flushing doesn't always work. Start pulling hoses and look in the coolers they usually get caught at cooler passages and they can make it all the way up thermostat. What I do when there are missing fins on impeller, start pulling hose from pump on till I find enough prices to put the old impeller back together then you known you got them all. Also check hoses from drive to pump. Is it sucking down while running. Also Transom can corrode and close off the hose where it runs through the transom this could cause your pump to run dry and might be what started the problem.

I had a thermostat go bad after having a impeller go out and engine got hot.