Here's a link to your thread from last year with pictures of what you have and also pictures of a PCM thermostat housing setup.

http://www.correctcraftfan.com/forum/forum_posts.asp?TID=49357&KW=&title=66-mustang-thermostat-housing" rel="nofollow -  link

Like mentioned in that thread it's a "mongrel" it's a PCM engine but the externals look to be Interceptor from what was probably the original 289 in the boat.

You'd be better off with a 140 degree thermostat when things are all straightened out since it's a boat in fresh water.

Maybe the port manifold has more rust and corrosion buildup in it causing it to get less cooling flow through it.

Are the hoses from the thermostat going to the manifolds pretty much equal temperature, they should be since the water to each is coming from the same place.

In the long run, you'd probably be better off with new manifolds and a PCM type thermostat and cooling setup.

PS Gotta love the old cars in the link too.  

Jerry,

Is this your engine from the previous thread that Ken linked? If so, the old Interceptors used dual cavity RWP's. One for each side of the V8 block so, you will have two RWP impellers. Open it up and check both impellers. 

Jerry 

Here's an old CCF picture of a 289 Interceptor (Reid P) with the same cooling system as yours with the yellow arrow pointing at the water pump. The silver thing is an oil cooler.

The pump on this vintage Small Block Ford Interceptor might just have one impeller. 

Or here's your picture with the arrow drawn in

In this picture you should have roughly the same temperature on the 2 lines with green arrows. That would be the temperature of water leaving the engine.

The temperature of the 2 lines with red arrows should be about equal and a lot cooler than the other lines because that's water leaving the raw water pump going to the engine and the 2 lines send some cool water to the manifolds. The port side with the oil cooler could be slightly warmer than the starboard but not enough to cause your issues.

If those temperatures are checked with an IR gun or your hand to be like mentioned above, then it seems logical that the manifold on the port side is the issue.

If you post your findings that'll help to figure things out.

Looks like the water pump interference issue is there in this picture of the other engine. It's in the same vintage mustang too, as a guess. maybe you can unbolt the mount from the engine instead of the pump from the mount .

Unbolt the pump from the engine, you shouldn't have to move it forward at all, just slide it up, down or sideways whichever works easier for you and you'll have the pump in your hands, then you can take it apart to get to the impeller.

I'd install the T stat. It will maintain consistant temps with different raw water temps like it's supposed to do. 

If you want to know if your cooling system works the driveway test is to take the water inlet off the bottom of your boat, usually this is one hose clamp, pull the hose free and insert it in a 5 gallon bucket.  Fill the bucket nearly to the top and start the engine.   Have your hose ready to keep the bucket filled as the engine runs.  A good working raw water pump will pull a normal flow through the engine, enough to empty the 5 gallon bucket in just a minute or so.  If your raw water pump is not working it will not pass this test in the bucket or on the lake.

I have had impellers fail slowly.  First sign is they will not pick up enough water at idle so temps start rising.  Speed up and the temps drop to normal.  On tear down the impeller looks good.  Close inspection shows that impeller has scratches on the vanes from stuff going through the system or they are stiff and shiny, just these scratches can cause the impeller to loose some suction.   New impeller solves this issue.   I live in the HOT west, impellers only last 2 years out here.   Run them 3 years and they fail and leave you stranded.   Age and heat kills them not the amount of use.  Maybe in Canada they last 10 years but not in Sacramento CA.   

Any leak on the suction side will cause the identical issues.  Every hose, clamp and connection has to be sealed tight.

As far as blockages causing overheats, yep, that happens also.  Someone may have had an impeller fall apart 3 years ago, if the chunks from the failed impeller get in the wrong spot you will have overheat.

Rule of thumb, if an impeller falls apart on your boat, keep tearing things down till you find all the lost chunks.  They will be in the cooling system somewhere and haunt you if you don't find and remove them.

The best $30 bucks you will spend is for a new impeller ever 2 years.  You will never have a failure.  We went on a 4 day ski trip with friends, one buddy had an impeller failure on the first day, he borrowed my spare.  After install the boat kept overheating.  I kept telling him to pull all the hoses and find all the chunks that were missing from the failed impeller.  He kept trying to shortcut the repair with no success.  Finally he took everything apart and found the missing chunks and his boat worked like new again.   As already mentioned the chunks can block the exhaust cooling or the engine cooling.   

I hope you have your boat ready for use.  Summer is here!

I think it was already mentioned but adding a "Timmy T" to your coolant intake line saves a lot of time and eliminates the need for a bucket to test your cooling system before taking the boat off your driveway.   I added mine several years ago.  Thanks to Tim Benjamin for teaching us how to add that nice tool.