Hi Travis; Welcome to the wonderful world of rocket science!
Tell us more about your home and its construction (pictures help).
There are options these days over what kind of
rmh you build.
There are these wonderful things called brick bells.(Stratification chamber) They are much more flexible in size and location than a piped mass is. Your floor may not need upgrading or as much.
They also can be upgraded to an 8" later, much easier than a piped mass.
I hear you about an existing roof jack being 6". Tell us more about your current chimney. Is it straight up and exposed ? Thin wall pipe or insulated? Or is it a block chimney?
There is also the new batch box style. They need some metal fabrication to build but they are superior to a J tube. With a longer hotter burn, using larger
wood that lays flat. A door that covers the whole thing so no exposed flames to the room and no chance of "smoke back"
These are things that can be easily retro fitted later if you don't limit things too much this year.
A 6" J in northern Wisconsin will need to run a lot.