John: We have some terminology issues here I think. I am assuming that by "deck" or "decking" you mean sole and by "reefer" you mean ice box. From this perspective I have some things to discuss. First off, if you do decide to strip the teak and holly sole before replacing it entirely, you must take great care. If it has de-laminated due to moisture, you are done. It cannot be brought back from this. If it is simply stained, you should be aware that the teak and holly is only a veneer and is very thin. I have had good success with a very sharp scraper or draw knife as some call it. I would carefully scrape the stained areas with the grain of the vener till I had removed only the polyurethane finish. A little trick with the scraper is to take a grinder and round the corners on either side of the blade. These rounded corners minimize the notching caused by holding the scraper off level when in use. Then bleach or clean the stained area using any of the available teak cleaning products, allow it to dry once the color matches the unstained portions of the floor and then re-coat using a polyurethane or varnish to match the original. DO NOT USE A MECHANICAL SANDER ON THIS TYPE OF FLOOR!!!! I hope I stressed that sufficiently. One wrong move and you can blow a hole through the veneer that you cannot hide. If you must sand do so with a block and some elbow grease, still proceeding slowly and carefully and always with the grain.
Sailors are a traditional bunch so if you ever wish to re-sell the boat be careful of straying from the original design or materials. I would never buy a boat that had evidence of extensive modification. I would try to match the original sole as best as you can, right down to measuring the width of the teak and holly strips and duplicating it exactly. This site has a lot of info about original materials and suppliers for this purpose. It only takes a little more effort to duplicate the builders or designers work and they spent many thousands of hours to get it right. Why mess with that?
Regarding the ice box, routing the drain to the bilge is an option and many builders used this method. That said, what you drain from the bottom of an icebox at the end of a voyage is generally not very pleasant. This smelly concoction will leave a residue in your bilges that you will smell forever. Your time may be better spent examining the through hull fittings and replacing them. Make sure there is a functioning ball valve on the drain and you can shut it off if there is ever an issue. Again, stock is best in my opinion.
The first boat we bought was in similar condition to Panacea. it was neglected but had really good bones and a great heritage. When we went to work on it we were a little overzealous and threw out a lot of junk that seemed to have no purpose only later to discover that some of these items were very important...and original to the boat. Take your time sorting through the junk and save everything for at least the first year. You will be amazed how many bits find a home at the end of the process. We wet sanded the gelcoat and waxed it and it came up like new...again this is on our site under "boats we have owned".
The most important and most satisfying thing we have done on very new boat we have bought was clean it. I would spend hours wet sanding or compounding the exterior and my wife cleans the interior with a toothbrush in the corners and vinegar and water or stronger cleansers for the really tough stains. Murphy's wood oil soap is great for cleaning woodwork. One really good cleaning takes years off of the age of a boat and helps familiarize you with your new vessel. You will be amazed how resilient the materials used to build your boat are. Don't be quick to remove or paint them. Once the interior woodwork has been cleaned and has had time to dry we would oil it with a bit of teak oil on a rag and go over the oiled areas with another dry rag. Once this has been done you will find that the remainder of the projects are not that intimidating. Avoid painting the hull or interior. One good cleaning often brings the boat back to a factory fresh look and smell.
The boat you bought can be restored to near new condition if you move through it carefully and systematically and do a bit of research along the way. Don't be too quick to make changes. So many new sailors take their boat and make it an RV on the water by adding microwaves, electrical doo-dads, lighting, tv's etc. Be careful of doing this. For resale, stock is best. Take her back to basics and then build on the clean pallet the builder and designer created.....in my opinion.
Hope this helps you.
Chris (the other Chris)