We sailed our 39' LOA schooner (draws 2'10") last April from Hudson, just north of Tarpon Springs/Anclote Key, to Apalachicola and then on thru the ICW to Mobile Bay.
Along the entire route you'll find very shallow water (3' or less) extending 2-3 miles from shore, and limited anchorages/marinas, generally spaced 30+ miles apart. To get to what anchorages there are, you'll have to navigate long, narrow channels through the shallows to shore (many of which are themselves so shallow, they cannot be navigated at low tide); and often then motor several miles up rivers to reach your destination - all of which adds a couple of hours on either end of your transit day.
Winds vary depending on time of year. Winters, winds are predominantly out of the north to north-east; summers, south to south-east. The shallows can kick up rapidly.
Our route was: Hudson to Yankeetown (on the Withlahoochee River); Yankeetown to Suwanee; Suwanee to Apalachicola. We by-passed possible overnights at Crystal River, Steinhatchee, Cedar Key, Carabelle and St. Marks. You are correct, at all of these locations there are limited opportunities to provision and fuel. There are small markets within limited walking distance at Hudson and Suwanee, and perhaps at Steinhatchee and Cedar Key.
Of the places we'd visit, the ones we'd return to are Hudson - cute little beach area, several good restaurants; and Suwanee, which was a small "old Florida" town and a beautiful river one could motor quite a ways up. We'd like to go to Cedar Key at some point; we skipped it this time because we were told the channels could be tricky and it's an anchor-only port, somewhat exposed (we had never anchored this boat before and didnt' want this to be the first time).
In between Suwanee/Steinhatchee and Apalachicola is bascially an overnighter given the distances. We considered going Suwanee to Steinhatchee and then across but the time/distance was about the same between each and Apalachicola. Our crossing was 25 hours dock-to-dock and we encountered much rougher winds/waves than predicted (a common problem all along the Gulf Coast).
We loved Apalachicola and highly recommend it as a cruising destination. Lots of old neighborhoods to stroll by, a nice nautical museum, and good shops and restaurants.
Many cruisers by-pass the Big Bend by doing an offshore passage direct from Apalachicola/Carabelle to Cedar Key, and then another to Anclote Key. Some do Apalachicola/Anclote Key direct. That will be our plan next year, when we plan to take the boat to the Keys for a month or so.
I agree that Rick Rhodes' book is a good reference to have on the trip. Make sure you have up-to-date charts for the area; there are quite a few obstructions south of Apalachicola, and there is a missile test range down there that occasionally is declared a prohibited area when missiles are being fired.
This is just an overview; if you'd like, send me a PM and I can provide more detailed info on the marinas we used.
Mike Turner
Lazyjack 32 schooner "Mary'Lis"
Mobile Bay, Alabama
