I've only burned soft coal (12K btu+) with a stoker but a couple things come to mind...The coal you're burning is a bit small for this stoker, I think pea coal would have worked better. With larger sized coal you could have the air set lower (or the same) and still be able to effectively burn all the coal in the retort. Smaller size coal can block air from reaching the center of the fuel bed. This results in the coal building up too high above the pot and the perimeter (or parts of the perimeter) of the coal fire to burn extremely hot....I suspect that's what happened here.
I would contact will burt and see if they still sell sectional tuyeres so you can replace the bad ones...I've heard that they may be discontinuing the coal stoker part of the business though.
I would burn soft coal in this in the future. If you don't want to use soft coal, or if it's not available, then I would burn pea hard coal.