Does anyone know how to get rid of a scratch on a kayak?

YOu don't need to fix it -- kayak hulls get scratched all the time and it doesn't affect their performance. I would not attempt a blow torch method -- you could cause real damage with that. Don't worry about the scratch and get used to it since you will collect more over the years, from concrete docks, hitting piers and submerged rocks. Heck, all my plastic kayaks look like maps of the world from all the scratches. Slap a coat of Scotch 303 UV protectant on the boat (it will help keep UV in sunlight from making the plastic brittle over the years) and the scratch will be less obvious. Kayaks are made to be used, not preserved. The "battle scars" go with the sport.

The holes are called "scuppers" and since you have a sit on top kayak they are to allow water to drain out of the hull. YOu can't really keep waves and paddle drip out of an open boat like that so the scuppers keep it from filling up.