I found that I was closing the boxes a little too tightly when assembling them. By pulling the front of the box back out, perhaps 1/8", I am able to fit diesels into the boxes, too.
It is possible to shoehorn a GP7/9 into an 800 ct box, by doing some cutting on the ends. I removed one layer of cardboard on one end and two layers on the other:
Interestingly, I discovered along the way that the newer traditional line GPs, with the horizontal truck-mounted can motors, are actually longer and will not fit in this modified 800 ct box! I suppose I can cut the coupler hole all the way through; or else order some 930 ct boxes.