if you are drilling holes, put a block of wood above and below to sandwich and immobilize the rubber. Just trying to drill rubber can cause it to catch and spin around and stretch or tear.
There are web pages where people Pasti-dip rubber boots to change color.
I am having that dilemma with riding boots that I want to turn into micronaut boots. Sand the boots first, then rattle can it. I would try to avoid anything rigid on the boot, like JB weld or screws unless that is your intention and you immobilize a large area around the hold (like 1 cm). The rubber boots will flop around and rigid materials will stretch and possibly tear the rubber.
Maybe post what you have and what you intend to do. There is usually more than one way to do all of this.