Hey Daniel,
I did exactly the same as you where I maximized the bricks more and leaving out the cutting for a minor change in dimensions. Although I don't have a Testo gas analyzer to verify how much this has affected the performance, a half season of successful use has proven that it burns clean enough for me and runs just fine.
My 6" batch box conversion thread shows my brick layout as I was gluing them together
here
Secondary air from the top will work just fine, its just much harder to replace when it craps out which was one of the reasons why it was brought down to the floor. Preheating the secondary air before it gets introduced to the fire and acting as an end iron to keep wood from blocking the port are two other perks the floor channel gives.
EDIT: BTW.... Those angled floor bricks were added to Peters design to help pool the coals together so that they would burn up more for the one fire he often does a day. Matt Walker has said though he leaves them out in his design because he does multiple loads a day and also makes it easier to clean. I have removed mine as I often do more than one burn a day and don't need this feature. No problem either way, but just thought you might like to consider it.
See
Stove Chat 14 at 39:25 where Matt discusses this.