This is the reason I've never liked ramboxes, they almost always seem misaligned. I found that there's a tool and instructions to correct this so I bought the mopar tool 2069900230 and adjusted mis-aligned ramboxes. My trucks passenger side was far worse than the driver
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I found a new tool on
ebay and bid $65 and it was accepted
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Passenger side before:
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Passenger side after:
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Driver side before:
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Driver after:
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Also found the 10MM ram box lid screws barely finger tight, adjusting them will allow you to move the doors in or out 1/4" helping them to sit flush with the body line. I'll probably mess with the driver side a little more to get it closer but both sides took about 30 min with the tool