Can We Change Our Minds Later?

You can and you will. What you are doing now is a big road map and its that road map that will help keep the current and future projects focused and organized.

You may never get rid of that masonry chimney but if it costs about the same to install a new high efficiency furnace then to line the existing chimney and you will need a new furnace in a few years anyway then why not make that change now? You will end up with a safe system, save some energy and open up some future options.