I was having an overheat on one bank on my 1986 V6 so I decided to do a little investigating. Take a look at the video on the link below.
Here is what I found when I pulled the T-stat covers and ran the motor. At idle even with a new impeller the flow of water thru the T-stats is not very much. If you look at the video right below the hole for the T-stats there are 4 small holes where water re-enters the head covers. The water then "falls" down thru the head covers and then I believe it goes thru the poppit valve. If the poppit is stuck open it would let the water exit the motor before the cavities in the head covers was full. Notice where the overheat sensors are compared to the water passage. I'd check the poppit valve first. Other than that do you know if the impeller was replaced with a genuine Yamaha part? I've heard that the Sierra's don't pump as well the Yamaha's do so I pay the extra for a Yammie part. Oh, and the pisser can flow what looks like a decent amount before any water actually flows uo to the stats. I noticed that if you rev up the engine and don't see an almost instant change in flow from the pisser then that means you are filling up the block before the pressure rises enough to see an increase at the pisser.
With all that said I also find that mine still runs hotter on one side when on the muffs than when its in the water. When you think about it when the boat is in the water at idle the pump is totally submerged. On the muffs you are relying one the hose to push the water up to the pump and then for the pump to lift it like 3-4 feet to the top of the block. I'd launch and see if you still get an overheat before you throw a lot of money at it.
Good luck, hope you get it resolved.
Steve P.
http://www.monkeybutler.com/boat/MVI_1589.avi