I use the Plano Waterproof 3500 size for my dropshot weights and hooks. It's the perfect size and a quality box, but my issue is the gap in between the dividers and the top of the box. My #2 and #1 Gammy dropshot hooks are now totally mixed together, which is no fun to sort out. Is there any modification to make that fixes this issue?

put your hooks on a paper clip or safety pin so they don't all move around 

Other than a small safety pin, no. Because of the way the lids made and meets farther down inside the box. Might try glueing a magnet in each section,you can get a pack that will fit the small sections at home depot.

1 hour ago, CenCal fisher said:

put your hooks on a paper clip or safety pin so they don't all move around 

I've tried that in other boxes before. Not a fan. Takes way too long to just grab a hook and I dropped them off the safety pin one too many times.

I cut shelf liner to fill in the upper portion of the box. My hooks never move from their spot anymore. 

 

i used some of the shelf liner too, glued to the lid and was skeptical at first....  aside from the occasional cross contamination on the smallest items in the box, it's nearly a perfect solution to your problem!