I have a Klein tool tray system in my truck. (6) tray rack. You should be able to custom design the drawers. I believe there are two sizes of drawers. Maybe not 3" deep.
Second look, large boxes are (3"deep X 12" X 18"). Click on the underlined phrases to link.
Pictured are the smaller trays. (2"deep X 9 3/4" X 13 5/16") Trays can be lifted out of the slide drawer assembly. There is a locking bar on the right side of the slide drawer.
This (6) tray and storage system dates to a 1990 Dodge Diesel truck that I had. Was moved to a 2002 Chevy 2500 and is now in a 2009 Chevy 2500 Truck. Pretty good stuff, that has held-up for quit some time. IMO.