Re: 15 ft 66 Falcon transom/deck repair
+1 for TDF's suggestion of replacing the whole stringer, and for the reasons he pointed out.
Think of deck, transom & stringers as parts of a whole system. And in terms of work & replacing them consider it this way:
If you needed to repair a fender on the car, which would give you a better result:
spot sanding, repairing, sanding the repair, prepping & re-painting just the damage & the smallish area around it?
or
sanding the whole fender, repairing the damage, sanding the repair, then the whole fender, prepping the whole fender & repainting the whole fender?
Which yields the result that will look better longer & that will last much longer before the problem returns?
Now imagine those repairs are being made to 3 of the 4 main structural elements of the car, and when in use you'll be in the water if a problem arises. The hull, transom, stringers & deck all work as a system to provide the structure of your boat. You can't just pull over when there's a problem while underway in a boat. As the owner, anyone boarding your boat, passively expects it to be seaworthy, and that you've done everything in your power & reach to ensure it's maintained & safely operated. That doesn't mean that carp doesn't happen, it does.
The least of my concerns would be how much more time & money it would involve to replace the stringers entirely. I am slowly putting mine back together because I have to spread the costs out over time.
It is a whole lot of work to remove the deck, replace the transom, make small repairs to the stringers cover them back with a whole new deck and not know that the stringer problems have totally & completely been resolved.
That's my $0.02 & is IMHO...