No idea how welcome it might be here, but I’ve worked up a tool to strip out most of the verbiage from the puzzle clues and identify the options purely by grid position. I did this after becoming frustrated with puzzles involving labels like long, barely distinguishable decimal numbers. It only supports 4×7 puzzles right now and is still a work in progress. Here’s the link: https://jsfiddle.net/Frungi/yus629ph/
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Wow, this is some clever work. I might be wrong, but I think you're in fact reversing what the website itself does. As I understand it, all the puzzles on the site are generated with a set of "master puzzles" that have their non-ordered label values (everything except category 1, based on your jsfiddle) shuffled; they're then assigned a story and the appropriate category names and variable labels.
I'm not sure that reducing puzzle clues to numeric representations will help with the average solver, but it could prove useful for puzzles where multiple categories share a label format (e.g. years sent and year received in "message in a bottle"; x-coordinate and y-coordinate in "geocaching"), where users could replace the labels with ones of their choice.
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