I'm using resin to seal up my exhaust cut outs where they were left as bare wood from the factory and the resin takes over a day to harden, where it's like a rock after about 20 minutes in the cup where I mix it. Am I doing something wrong here?

I assume since it is an exothermic reaction, the heat that is given off in the confined space of the cup makes it cure faster. And the faster it cures the more heat is given off. Then the curing goes exponential and the cup gets really hot.
There is my guess.

That is exactly why. But it shouldn't take a day to harden on the cut-outs. What type of resin? Sometimes epoxy in thin layers can take awhile to fully cure, depending on the hardener used and ambient temperature.

I'm not sure, it was just a small metal container that they sold at west marine, came with the separate hardener in a little tube. The first coat was definitely still tacky after 6 hours yesterday while the cup hardened in about 12-15 minutes

the key is to keep your working cup/batch small.

when i use west tec epoxy with 205 hardener (fast) i usually only pump 4-5 pumps at a time. keep the batches small and you can refill all day long with the same cup and brush without it kicking. if you pump/pour a quart of resin its gonna go up in a blaze of glory in your cup just trying to mix it. i get a good 30 minutes of working time with it before it starts to kick on me in 70* weather.

shallow bowls have longer working life than deep cups.