Looking for some ideas.

I cant keep an exhaust flapper on the port side of the starboard motor more than 1 hour of operation. You can smell the rubber burning from the exhaust boot and the flapper at WOT. The starboard side of the motor is fine and runs very cool. With the closed cooling system, it seems the restriction would be somewhere in the exhaust system on that side, been flushed and flushed and taken apart and cleaned, all with no success. Looking for ideas at this point.

there is no water flowing thru the port side exhaust or very little ..... pull the hose coming from heat exchanger and compare flow to each side. Sounds like the exhaust itself might have blockage ...... more details on just what setup you have and hours ....ect ....m

2008 42' lightning with 700 mercs approx 48 hours.

No warranty?

Yeah there is a warranty, but I'm tired of flushing the raw water system and putting a new tip and that being considered "fixing" it. Been through three tips and one exhaust boot and system was flushed every time. New impellers installed right after Destin. Problems started right after the boat was put on the beach in Destin. Makes you assume sand is the issue but it seems a flush would eliminate any sand and the problem being localized to the port side header is what really throws me.

Flushing will not remove all the sand. Get somebody to do the job correctly. Take the exhaust off the motor and make sure it is clear and has good flow.

Is there a way to use an infra red temp gun to see where the temp goes up, then maybe if possible to back flush the area with out flooding the engine. I have backflushed many a cooling system with good results.

Probably marginal water pressure. The 700's need to run at more than 30 psi to get enough water through the headers and intercooler. If it gets a little iffy, a header steams in the water jacket and that acts like a blockage causing most of the water to go to the other header and tailpipe. Sometimes a long tailpipe can steam cause the same issue even with enough pressure. The longer tailpipes have trouble filling and can get a hot area on the top that can start the water in the jacket to steam. The steam creates a lot of internal pressure in the water jacket which blocks water flow and it just gets worse.