Removed 0.5mm of the lid hinge on both sides, totaling 1mm less material to deform in order to install the lid. I find that this still holds in place without problem.
Removed 0.5mm of lid thickness from the side that touches the bits. I found that the original wasn't able to close fully because some of my bits are say, 25.6mm.
And lastly, I made the latch sit more tightly around the bump on the case. The original was rattling, and would open from the weight of the box contents if moved the wrong way. This holds closed for me.