I have no problem deciding when to pull fish fillets out of the
oven so as not to overcook them, but I have a *much* harder time
getting it right with whole fish. This is largely because I want
to be able to carve and serve nice fillets from the fish (so I
don't want to hack too much into it).

Now, I absolutely *hate* overcooked fish, but I'm not wild about
undercooked fish either (with the exception of sushi/sashimi, of
course). How can I tell when I have reached that magical point in
which the whole fish is cooked all the way to the backbone, but
not overcooked? Is it even *possible* to bake a large whole fish
(say, 3 in [7.5 cm] thick) so that all of it is cooked, and no part
of it is overcooked?

My book ("Fish & Shellfish" by Peterson) instructs to "[c]heck for
doneness by carefully sliding a paring knife into the back at the
thickest part, gently lifting the top fillet, and peeking inside
to make sure the fish pulls away from the bone and the flesh is
opaque (but still moist) rather than tranlucent and raw."

Well, the other night I did just that with a 4.5 lb (2 kg), 3 in.
(7.5 cm)-thick red snapper, which I baked at 400* F (200 C) for
about 40 minutes. When I peeked inside, the little I could see
(opaque flesh) suggested that the fish was ready for carving. This
is a nearly irreversible decision in the case of a big whole fish,
especially if you want to serve nice fillets (it so happens I had
guests over at the time); it entails transferring a big fish from
roasting pan to cutting board, and removing the hot stuffing (lemon
slices and herbs in my case), not maneuvers one wants to undo, and
of course, making deep cuts into the side of the fish. Unfortunately,
my judgment was off. When I served it, the meat was rather soggy,
especially near the fish's backbone; it did not separate cleanly
from the backbone, i.e. it was somewhat undercooked.

Any advice would be much appreciated.

Thanks,

Irv