it's a bit of a rough M$ Paint picture....
but couldn't something like this be used ?

you could even have it outside as long as it's well insulated
if it's below your heat store/tank/whatever it would gravity feed / work by convection pretty well
could even be plumbed in via heat exchanger if you're worried about acid etc.. burning though the pipes...
takes care of everything ?
coil extracts the heat from the flue
drain is there incase of condensation
I know there's the worry of the acidic condensation / soot build up... but there's been enough posts by people with copper coils jammed into there flues to make it worth a go... and as long as the add on section of flue with the heat exchanger in it is sized about right then there's shouldn't be too much soot build up ? (could be a good idea to test it for a few weeks with no water, and check it for soot build up, then it can always be adapted without too much hassle ?