Now that you point it out, I see I goofed on the cad file. The windows are about 1.5mm too low, and the roof access door is about 2mm too tall.
I took the design from some pictures I found online. Turns out it's the Walthers HO Cornerstone Grocery Distributor.
Hoping to test some more window methods after cut the silos on the Roca, NE Elevator and Storage tonight.