Personally, I would cut it in the middle giving you equal area on both sides to run doublers or stringers. Also keeps the integrity of the firewall intact, and easier to line up the "two halves" of the motor box to keep all the thrust angles the same. If you use triangle balsa stock in the corners, it almost does this by itself.

We have used motorcalc a lot . . very helpful with getting everything close. Nothing is the same as actually flying it and playing with props / batteries, etc . .