I have found myself in a similar situation. I have a central chimney which is structurally unsound. In attempting to avoid the high cost of replacing it (chimney contractors seem to shy away from this subject when I mention it), I was wondering if I could just remove it to the second story, and then run a liner from the furnace up through the existing cavity to an exaust pipe on the roof. My greatest concern is that this will violate some building ordinance, and could really use some professional advice. I do not believe that removal of the chimney will weaken the roof rafters.