Richard,
Nice boat; definitely a BB2. And judging by the condition of the bottom of the boat, it's not been run hard. I've built a BB2 and Broadbill, and am in the process of wrapping up a Cackler. Love the BB2; have had it out fishing the last few weekends.
My boats have mostly been garaged, so, I've not had a whole lot of repairs to do, other than some minor work on the Broadbill. However, will offer some thoughts. Most of what I know is through the school of hard knocks.
Sounds like you are off to a good start on addressing the problem. First priority would be for finding any exposed wood and dealing with it. That includes screw holes, cracks, gouges, rub points, delamination, etc.. Exposed wood rots; sealed, dry wood is very durable. I'd also try to figure out what is going on with the floatation compartments (are they watertight, and, are they filled with foam?). There have been issues with some boats leaking water into the compartments and saturating foam. With no knowledge of the history of the boat, I would cut a hole in each compartment to check it out and install deck plates to inspect at later times, but, that is just an opinion. You can do a search on this site, and will see wet foam can be ugly.
Also, check the knees at the most interior point where they join the hull for cracks. This has been a weak spot on some boats, but may not be a problem on yours. If cracked, you can repair with bigger fillets and new fiberglass tape, or go stronger with a floor beam, other floor support structure or even bond floor the floor in place.
Anywhere hard items rub epoxied wood, there can be a problem, like your floating floor support contact points. I originally was trailering my Broadbill on plain wood bunks; the vibration and grit ate through the paint and started eating into the epoxy. I fixed that, swapped to a new carpeted trailer, and even after extensive trailering you cannot tell where the carpet supports the hull. Fixing the inside of the hull is easy; just sand and apply 3 coat of epoxy. Another option in my opinion is you could place glass over the area, just like top coating the deck. I did find some fine line cracks on the inside floor of my Broadbill after using it for several years. I sanded it and put a layer of thin glass and 3 coats epoxy. Based on that experience, I glassed the inside floors of the other 2 boats while they were being built. You might consider a flexible cloth that can be used with boat building epoxy work; I think Devlin recommends Dynel now. You need to look at other options for floors support, or, at least putting some foam strip at the contact points. The floor in my BB2 is loose (I like to be able to see what is going on under it). However, I ran foam weather-strip along the contact points to avoid damaging the epoxy and exposing wood.
Not sure why someone put long screws through the keels, but if at all suspect I'd take them out and fill with epoxy/wood flour. If the keels are properly epoxied in place, the screws are of no value.
As for the runners on top the keelsons, just replace with like (looks like you have 1/8" aluminum, which works very well). Bed with 5200 and use 1/2"ss screws per Devlin's plans to hold in place. There are other options on keels if you do a complete rework, but what you have works well.
For the rub rails, I am hoping someone who has done restoration chimes in. I have only see fiberglass peel off like that on the maple I used for the oarlocks on my Broadbill. My plan is to replace them with Doug Fir, which seems to absorb enough epoxy to prevent any delaminating. Using the right wood seems to be the key for building a durable epoxy encapsulated wooden boat.
You can sand and fill with fairing compound to take the fiberglass texture out of the boat, if desired. Just keep in mind removing material is removing strength and moisture barrier, so you cannot sand too much or you will need to add more fiberglass/epoxy.
Oh, and since you have a BB2, you may want to put on your motor, then move the it from the down position to the full up, while turned completely left or right. If the anti ventilation plate hits the sponsons, you may want cut the lower inside corners of the sponson to make clearance so as not to damage your engine it kick up. There have been several posts recently of BB2/BB3's that have had this modification done.
Have fun with the boat- looks like you got a good one!
-Bill