I do leather work, in those boots that take severe abuse, they get smooth spots in the extreme wear areas and the two smooth surfaces rubbing together make the squeak. Like rubbing a wet finger on glass. Your first idea is the best, find those areas and rough them up with sandpaper but be careful not to nick or scratch the stitching, which will continue to fail over time if damaged. If you do nick or scratch them, hit them with some superglue and smooth out when wet. Like these guys are saying, keep some pitch blend with you in your pack. If the surfaces are worn smooth again on the hunt, it will take away the squeak. Although Gore Tex can be affected if exposed directly, this layer is protected well inside the boot. The mink oil or pitch blend rarely ever makes it in that far into the leather to permeate the lining. If it does, it will only happen in a few spots and shouldn't effect the overall breathability of the membrane. Funny how they always start to squeak just as that big bull.....