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I hate to bear the bad news, but there doesn't seem to be a good way to make it look right. 54 bedsides have the embossed pattern that follows the top of the angle strip, making it hard to move the angle up. If you move the whole bed up it does not look right with the cab and running board/splash apron. It sounds like you are heavily invested in the rest of the truck, so the bed should be quality to match.
Suggest you try to sell the 54 bed and look for a good bed to match the frame. That 54 bed in good condition should not be too hard to sell, since they are unique to 54 and 55 1st series.
Mar-Ktech
