For the past half dozen years, I have over-wintered on Chokoloskee Island. We typically navigated from Everglades City south to Lostman's River; and also from Flamingo west to East Cape Sable. However, we were not in our C-Dory, but our Hobie sailing kayak (with a small outboard). We used the kayak for providing the best access to fishing in the very skinny water--both through the 10,000 Islands and down the Wilderness Waterway.
Indian Key Pass from Everglades City is easy to access by boat (strong currents during large winter tides). Be sure to eat at Camellia Street Grill in Everglades City (has dock on the water)--esp the fish tacos. The Havana Cafe in on Chokoloskee Island (dock at very high tide at Chokoloskee Island Park Marina via Chokoloskee Pass and walk 2 blocks) is also terrific. If you can navigate Chokoloskee Pass, then you should be good-to-go the rest of the way. Probably don't tempt fate by taking Rabit Key Pass going back west/south.
Also, just west of Everglades City, Port of the Everglades is navigable to the islands (as is launching out of Goodland). Be sure to stop by Pavilion Key (the outside is much deeper than the inside). Once you get south of Chatham River, the rivers would be your best bet for more protected anchorage--though you may need to be on a rising tide to safely enter them--esp if off plane. The fishing charter center consoles do it all the time--they usually run on-plane to keep the prop above bottom--and they know where/when to (not to) go.
My initial calibration to such skinny water was coming into Flamingo and admiring all the birds way offshore. Then I realized they were standing.
I found two books helpful. "A Paddler's Guide to Everglades National Park" by Johnny Molloy. and "Florida Circumnavigational Saltwater Paddling Trail Guide" by FL Office of Greenways & Trails. The Florida State book has the text descriptions--and you download the maps you wish.
Everglades National Park requires a boating certification, that you can complete online.
https://www.nps.gov/ever/planyourvisit/boater-education-program.htm
Hope you are able to make your trip. Coming out of Everglades City and turning south with 100 undeveloped miles in front of you (either inland waterway or gulf) is a pretty remarkable way to visit Florida.
I am sure the local Florida folks will join in with better specifics.