The Safe (with fixed handle):

Inside:

Inside, under the cover with lock bolt retracted (door bolt extended):

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So... why did the handle fall off? The as-found shaft appears to be much too short for the aluminum handle. There was less than 1/2" engagement. My working theory is, over time, the force needed to pull open the door eventually wore out the ID of the handle, causing it to be excessively loose and wore out the match drilled/match tapped holes. The door does bind a bit, depending on how loose/tight the bolts are. More on this below. Once the handle retaining screw fell out, the customer then started using a Cotter pin to keep them together. This just increased slop in the handle and destroyed the threads. Apparently, they broke the cotter pin every months or two. Each day wore down the aluminum just a bit until it was just... floppy.
I am also wondering if the old handle shaft was broken during an attack because shaft at the fork weld looks like it was snapped off, and the weld is... ugly. (3rd picture above)

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The fix done was to weld on a 1/2 steel piece to the shaft to increase the length approx 5/8" longer to fully and snugly engage the handle inside, and match drill/ream for a press-fit dowel pin all the way through. The handle should not go anywhere unless it is intentionally removed by driving out the pin. If the pin and handle becomes loose with abuse, Loctite is still an option.

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One reason contributing to the wear inside the handle is that the door alignment is not quite right. The 4 bolts are "just a bit loose" because if you tighten them nice and snug, the door moves left upon tightening and binds tightly at the left and bottom. Looking at the closed door, the gap at the top seems larger than it should be, and there is also a gap at the bottom of the hinge. The bottom of the door and top of the hinge have no gap.

Here is the question: What is likely the best way to properly align this door?
Should there be a thrust washer (or brass shim/spacer) underneath the top hinge to better lift the door into alignment? Presumably, a spacer under the top hinge will pull up the door, and better center it in the opening so that it does not bind up anywhere. Or, do I just need to put shims all the way around the door with the bolts loose, then tighten the 4 bolts with the shims in place hoping the door does not shift again during tightening?
Thanks for making it this far. Any advice is appreciated.
~Blue