We did this ride last year, except that we started on the East coast of Florida, rode to Key West, and then we were going to take the ferry to Fort Myers and ride back. EXCEPT, the ferry captain, after we had called ahead and reserved tickets and explained that we had bikes and all, denied us a place on the ferry. I would not trust the ferry as a way to get from Key West back to Fort Meyers, but you can always try.
As a side note, hotels are extremely expensive in Key West, and we could not afford to spend another night there, but we were stranded due to the fact the ferry wouldn't take us. Luckily, we found a big enough rental car and drove back to the main land in one night. The car ended up being much cheaper than the ferry anyway.
Anyway, the ACA does print the Florida connector map like alan said. It is probably the safest way to get from West to East coast of Florida, but it is not extremely scenic. We found an alternate route that is a bit more scenic, but probably more dangerous due to some narrow shoulders and truck traffic. It is called the Tamiami Trail, and it goes from Fort Meyers to Miami. It will take you through Big Cypress National Preserve, and you will get to see a good deal of wildlife. Really the Tamiami Trail was not bad at all. The worst part of this ride for us was the section through Miami on the Atlantic Coast. There traffic was terrible for about a 20 mile stretch through the city. Easily the worst riding conditions I have experienced on an Adventure Cycling route.
Not to deter you though, overall the trip was great, and the Keys were great fun to ride through. The temperatures were amazing every day, and Key West was beyond fun. Be sure to plan out where you will stay each night, especially if you are camping, reserve in advance. The camping down there fills up very fast. You can check out our blog in my signature if you would like. There we documented our trip last winter.