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What kind of fiberglass cap did you remove? When I hear "cap" I think of a roof-height box that sits on top of the bed rails and gives the truck a more Suburban-like appearance, or possibly a higher-roof work/camping top like zerohour mentioned.
Even if the cap is roof height and you have no additional cross-sectional area, the cap will make your drag coefficient worse. The large, flat rear vertical wall of the cap plus tailgate gives you a large wake area. With an open bed or a tonneau cover (flat, bed rail height bed cover) there is a tiny wake behind the rear glass and your main wake that is the area of the tailgate. A taller cap gives you larger wake plus more frontal area, destryong your Cd and increasing your A, so your total CdA is much worse.
My personal experience has proven to me that the longer the bed the more important the bed treatment is for aerodynamics. I drive a truck with a 6'-3 bed and have a soft tonneau that yielded 1-2 mpg when I bought it. My brother-in-law has a Tacoma with a 5' or less bed and adding his tonneau didn't make a difference. I once towed a home made 16' flatbed utility trailer with plywood walls and tailgate and I was getting 12mpg at 60mph until I removed the tailgate, at which point I went up to 16mpg at 65.
I think zerohour's hypothesis about the plane of the toolbox affecting how the bed bubble shields the tailgate from contributing to drag area has merit, but short of throwing a bunch of sand into the wind at highway speed I'm not sure the best way to test it. Adding a soft tonneau and watching how the fabric stretches can show you where the low and high pressure areas are, and if you aren't getting a high pressure area (fabric being pushed down) just in front of the tailgate with your toolbox then that must have been what did the trick, and a tonneau might not make any difference.
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