If the wall between rooms is load-bearing, you could get by with cutting a 20cm wide x say 30cm high slot near the base for the gases to flow from one side to the other, without any problems.
As Cristobal implies, the best setup would be a combustion core (J-tube or batch box) in one room, probably the lower one, inside a masonry bell of about half the size calculated for your heating load, leading through the wall to a similar bell on the other side, and then to the chimney. You can build the bells as three sided boxes with the existing wall making the fourth common side, to minimize space required. The core will require certain minimum horizontal dimensions inside the first bell, though part of the core can stick out if necessary. The second bell can be any shape that gives the right internal surface area, such as wide and flat to the wall, possibly projecting as little as 30cm.
Given appropriate planning, you can build an easy J-tube to start with and then convert to a batch box with very little waste when you have more time and experience. J-tubes do not require all of the wood to be split small; the bulk of your fuel after starting can be sized such that 3 or 4 logs will fill the feed tube.