Your truck appears to be altered from stock. The stock wheelbase of the shortbed truck is 115". Your's looks longer by a few inches. You might have a newer truck frame under your sheetmetal. The bed also seems to be extremely close to the cab. But that just may be the picture. There should be at least 1" between the 2.
A workaround might be to simply remount the fenders to the rear by several inches.
Take a peek at this stepside from the gallery and compare the wheel locations relative to the fenders.
http://www.stovebolt.com/gallery/images/clark_bob_1961d.jpg
Your bed may have been remounted too far forward. Have fun.