Hi Tim, I had twin 45hp Hondas around about 10 years ago on a humber rib. They were fairly tatty, high hour engines that i got cheap and refurbished myself. But had one or two problems with them over the years. One of them would not start very well when it was hot, and balancing the carbs and re-setting the fuel air mixture screw settings cured that problem perfectly. But the second engine nearly drove me round the bend
It had a problem that sounds very similar to yours. It would run great and strong at speed but, slow down to idle and it would slowly die down untill it stalled. I re-set the carbs like i did on the other engine, no difference. I took the hood off and upped the idle speed a fair bit so there was no way it could stall, sounded great, put the hood on, took it for a run, pulled it back to idle, stalled AGAIN
Then i took it for a run with the hood off, and beleive it or not, it idled PERFECTLY! Put the hood back on, it would slowly die and stall.
To cut a long story short, the Exhaust had corroded through, and there was a small 5mm hole where the power head bolts to the block, The exhaust gas leaking out under the hood and was being ingested by the engine, and it won't idle very well with a build up of exhaust gas under the hood. It would have cost a FORTUNE to fix properly, so we just put a little Chemical Metal over the hole and it cured the problem fine, Idle was perfect after that. The engine ran great for many years after that. Anyway, perhaps worth trying a run without the hood on your engine, just to see if your engine has the same fault. Also if you are still having problems, Can i highly recommend giving Colin at Ardoran Marine in Oban a ring. He's a Honda 4 stroke expert and gave me loads of very helpful advice when i had my problems.
Hope this Helps