Make sure you don't have your frame in a place that would put the box corners where the tubes start to curve in. If you do, it's okay but use the inside width from the curves, not straight sections in that situation. Some people like the box touching the sides. I like to leave an inch on each side so it's easier to take in and out (I carry the kitchen sometimes). Much more than an inch and you're losing space and will drop things down there. Height, you rowing off it, rowing off a paco on the box, using a seat, etc? Mock up the height you'd like to row from above the frame, than add the distance to the flow (below the frame). If for passengers to ride on, do the same but it's not as big of a deal. I like leaving a couple inches between the floor and bottom of the box because we run some boney rivers and I'll run a soft floor. I like a little margin of error if I go over a rock so I'm less likely to pinch my floor between a rock and a box or cooler. Some people have their boxes touching the floor. Personal preference. Length-how big can you go without cramping your rowers compartment? Go that big. Also, if you have certain big items you know will go in the box (big boiling pot), make sure that will clear the inside lip of the box.
Nobody on the internet should be able to tell you exactly what size to get the box from the info you gave. They can tell you how to measure things out so you are happy with what you buy.