After a few measuring errors, and one really lopsided milk carton, I think I finally got it!
I took a picture of both boxes to show the difference in size. There's lots more room for treats in the taller one!
To make the tall box, follow the instructions for the small box here. The changes that need to be made are:
The paper you use will need to be trimmed to 11" x 11.5".
Step 1 changes: score at 1/2", 2.5", and 9.25"
Step 2 changes: score at 1/2", 3.25", 6", and 8 3/4".
Hope that makes sense!