After my failed attempt at stapling the magazine, I stitched the upper bit together where I already had the holes, which didn’t look amazing but worked okay. After doing that I tried stapling the bottom bit, I thought even if it would fail, I needed the holes for stitching so nothing to loose here, and all of a sudden it worked! No idea why, maybe the magazine had become flatter in the few hours in between testing or something. Anyways, it held together so I took the thread out of the upper bit and stapled that too.
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