Unless others disagree here or elsewhere on the web, I'd be inclined to follow the Moyer-recommended procedure here:
http://www.moyermarine.com/forums/sh...highlight=acid
I'm relatively sure that is what the previous owner of my Atomic 4 did, with sucessful results. Sounds like it sits in the engine for only 15 mintues. I don't think running it through the engine for several hours is an option, unless you looped the system, and even that could cause overheating.
As for the environment and disposal, here's an interesting comment from Moyer:
http://www.moyermarine.com/forums/sh...highlight=acid
I'll admit that when I've used muriatic acid to clean old toilets, I haven't worried about the flush since it didn't seem terribly strong. The suggestion in the first link above about capturing the 5 gallons of diluted solution and treating with 1/2 pound of baking soda before disposal is also interesting.
Anyway, before doing the acid bit, I'd want to find out what's up with the water pump pressure. It's possible that even with a new impeller that the pump could be weak.
Good luck!
Jim H