Congratulations on your new boat. I’ve spent a lot of time on Rascal, and she is a very good boat. With regards to the life raft cradle behind the mizzenmast, I would remove it. With the life raft in the current position, you would no t be able to rig and use the emergency tiller should the need ever arise.
Unless you are very good with fiberglass and gel coat work, I’d hire someone who is to fill the holes. It is not going to be easy to match the repair to the current deck, and it will require someone talented in this type of work to make that happen.
Best of luck with your new boat.