Bryan has it right. The damage looks worse than it really is. The only major concern would be that crack in the seam. If the wood is rotted, then you have two choices: (1) replace it (bit of work) or (2) clean out the rotted wood and if the area to fill is small, thicken epoxy with wood flour made from similar wood and fill it. If the rot is bad enough, replacing the wood is the ideal way to go. You will need to glass over this particular repair job top and bottom, for strength. Take a very careful look at the insides of the kayak as well. Odds are there is unseen damage there as well.

Working with fibreglass is a piece of cake, like putting a bandaid on a wound except you glue it down with marine grade epoxy, let it cure and sand it smooth. The other delaminated areas can be sanded clean to remove the old glass and expose the clean wood and reglassed. The re-glassed patches can be sanded with feathered edges and finished to look like new. You are looking at a couple of weekends of work, possibly a bit more but the effort is relatively minor once you know what to do. There are many excellent folks here with decades of experience. One note: if the colored areas are wood dyed, it will be tricky to restore the color. Hopefully someone here can advise you on that aspect of this repair. Varnishing the repaired kayak will help protect it from UV damage from the sun. Use 5 coats of varnish once the boat is ready.

Looks like you got a sweet new ride. Congrats on the new baby.

Robert N Pruden