If you're making a 6" system, the brick core can be 6" x 6" inside. A factor overlooked by early experimenters is that square channels have more drag than round channels of the same cross section; 6" square and 6" diameter are about equivalent in actual drag. A 5" x 5" square channel would have significantly more drag than a 6" diameter channel.
For brick stacking, you generally want them on edge instead of flat both to minimize material expense and to make the dense material thinner. You can't make a brick stack exactly 6" high without cutting, but one firebrick flat at 2 1/2" plus one on edge at 4 1/2" gives 7", and you can make the feed and burn tunnel say 1/2" narrower. This will allow for a half inch of
ash to stay on the burn tunnel floor which will insulate the floor some more. You can then go to a 6" x 6" heat riser. The little steps outward on the sides will, if anything, add a touch of turbulence which is good.
The burn tunnel and lower third of the riser see the highest temperatures, so those are the places to concentrate firebrick if you have to choose.