For what it's worth, we did the trip last January and here is where we stopped along the way. Each stop was a day sail from each other and there was no drama except for the crab pot we picked up. So, what out for crab pots and you'll be ok.
1. Pelican Bay....great spot, lots of room. The channel into the bay is only about 50 feet from the beach, trust the channel.
2. Moss Marina...we only stopped here to get some quick work done.
3. San Marco Island...crowded, but beautiful. Found a spot in the back.
4. Indian Key. another great spot
5. Little Shark River...If you want solitude then this is the place. No cell service
. Really pretty, but can get buggy.
6. Marathon...Boot Key Harbor...We enjoyed Boot Key, some folks don't due to large amount of people there. From Marathon we made our way up the Keys to Miami
and the ICW
Hope this helps a little....Sid