Jim's idea worked like a dream. Using the old Emmert woodworking vice I inherited from my Dad, straight edges and clamps, I secured the front bed cap and trimmed the bottom flange off using my cordless jigsaw.
Gap was a bit too wide so I spun the vice longways and squeezed it down until I closed the gap enough to create a tight friction fit. The bed cap twisted after I cut off the bottom flange, so, with help from Jim, we twisted it back to about 90% straight. The rest of the straightening will happen when I tack it into place.
The worries I had about the unnatural looking flange running under the end cap went away. The shadow created makes and imperfections disappear. Looks pretty factory to me.
Added shim to the center at the cab just to straighten up. Gap is pretty close at about 1/2" but should be fine.
Will set it permanently to the '95 bed when I get the bed sides hung. As I mentioned before, I plan on making a flange and bolting it to the top of the bedsides temporarily (semi-permanently??). I want to make the bedsides removable until I can get to the body work.