Useful assistance appreciated

We have had several old boatmen who have come by to offer a thousand suggestions and great advise on how to proceed with this "huge" project. Some of them had seen the boat sitting in dry dock idle for several years and were ecstatic that someone had bought her and is making her sea worthy and beautiful again. One boatman showed us tools to remove caulking make out of old files one day while we were on break and so we have had some made and are ready to start the big job of scraping out old cotton and caulk, and replacing where necessary. Any ideas on how to make "plugs" to put into the holes left by the countersinking of the original square nails that were used to build her? The depth of the holes are only about 1/16"..Would epoxy mixed with some teak sawdust work alright? One great source of information has been a gentleman in Florida who owns a Junk also. We appreciate and love to hear from everyone about this project since we have built houses, stagecoaches, and other wood projects before, but never a boat. We will also have to learn how to sail her yet.

We finished our trip to Kentucky and Tennessee and are now on our way back to the Marina to get back to work. We have parked our RV close by so we can start nice and early in the mornings and even sneak in a nap!