I built all the way to the top layer of straights before I realized the problem. As you can see, if you follow the vertical line of the edge of the flue upwards, it butts right against the soda ports. Which means the soda ports will be hidden behind the stack wall. Nice going there, Ace! I spent a day trying to figure out how to rework the stack or the ports before I decided that was too much power to give to a mistake: better to correct my error than compound it.
So Thursday I took the back wall down, built the flue as I should have in the first place, soap-cuts and all. By this time I am an old hand at cutting hardbrick with a chisel, and though it was slow going it wasn't really difficult.
Lessons learned: 1) Don't make design changes on the fly; and 2) the difficulty I am trying to avoid might not be the big deal I think it is.