Congrats on the recent purchase. Good luck with her.
If it was me, here is what I would do:
1) The water coming into the deck is the first problem. This is likely leaking around penetrations for deck hardware (i.e. the bolts that hold down stanchions, cleats, jib tracks, chain plates, etc.). This is called "re-bedding" and is not uncommon; I have a 2001 Catalina 310 and I have to deal with this issue this spring. I would suggest you go to Maine Sail's site
and searching these forums for details on how to do this.
2) If you core damage around the deck hardware, you should fix this before you re-bed the hardware. Again, not uncommon (I have this issue around one of my stanchions). And again I would recommend you look at Maine Sail's site and search the forums for details on how to do this. It is called "potting".
3) Then, if the deck damage is bad enough, look at the epoxy injection or core replacement.
Hope this helps.