if they get $1100 for flushing the raw water side, i'm quitting my job and starting a marine handyman business TOMORROW!
i'd have to guess the quoted price is to flush the closed cooling system. a neighbor at the marina with a 1990 silverton with crusaders did this when he first bought his boat. he did it himself several times b/c he found a surprising amount of crud in there each time he drained it out. apparently, the prior owner of his boat really neglected it. there's a hard to reach plug beneath the engine that needs to be removed. you drain and collect the coolant, close the plug, pour in water and some chemical made for just such a job (radiator flush??), then run the engine, drain and repeat. not rocket science, but i'd imagine the HARDEST part is getting that drain plug. you could probably also do this by pulling some hoses and draining, adding water, and repeating until the coolant is almost totally diluted, but that would be more time consuming.
could you rig something up to draw water from a source (bucket or hose) on one end of the system, then pull a hose at the other end of the system and collect the water/coolant from that point. run it til it's clear, the add new coolant? the problem i foresee here is you never really drain the system completely so how do you know the ratio you are entering back into the system when you refill??