Since you have plenty of time to plan your trip, the other thing I would consider (because I have done both ways) is this: Once you're inside FL on the AICW, how do you intend to arrive in the keys, and where will you reside in the keys? Two, IMO, possibilities exist: (1) Cruise the AICW from Stuart south, come out at Biscayne Key, make the turn at Key Largo and dead-head to the Keys; or, (2) consider the Okeechobee Waterway where you'll begin in Stuart, and arrive near Ft. Myers (Sanibel Island) and you can dead-head to the Keys or the Dry Tortugas.
I've spent oodles of time both SCUBA and fishing from Key Largo to the Dry Tortugas with several friends (and boat builders) residing in Islamorada, Marathon, Bahia Honday Key areas. If you do SCUBA, there are some fine stone crab claws to be obtained (during the season) at Sombrero Key, Loue Key and Bahia Honda Key along the coral reefs at depths no greater then 35'. Additionally, some very tasty spiny lobsters during season - my favorites - delicious, not much meat (more like crayfish) but very, very tasty and very easy to catch at night. Lots of great flounder to be had, as well.
Tons of boatels to choose from, as well. You might look into boatels as an option for where you intend to reside for periods of time. They make life very enjoyable when you can get up, get on the boat, and cruise.
I personally love viewing the spectacular homes on the AICW in the areas of Pompano, Ft. Lauderdale, and Miami - when I have the time. Some of the glass museums owned and maintained by several owners (in their backyards), and at least one house with an underground bedroom with portholes into the AICW are well, they're pretty wild. My point here is this. The homes, and the AICW in this area are remarkable - I have witnessed it change since the first time I travelled the AICW in the Pompano, Ft. Lauderdale, Miami area since 1969 - and, change it has - spectacular - but you're going to find it very, very slow. Mostly no wake zones (for very good reason) extending nearly the entire course of travel in this area. Once you pop out of the AICW, in the general area of Biscayne Key, you'll be dead-heading for the most part to your destination in the FL Keys - wherever that is.
Not sure if you SCUBA or not. When you make the bend around Key Largo, there is Jules Underwater Lodge. I recall when it was built. I've several friends who have done the overnight - and, said it was "pretty cool". I have not done it myself. Just thought I'd toss it out as an alternative accomodation if you're the adventurous type mate!
http://www.jul.com/frontpage.html
Finally, don't forget mate, fall is hurricane season. I don't want to draw unwarranted skepticism into your plans. Use diligence regarding what month you intend to leave in the fall and just keep a mindful eye on the North Coast of Africa chap!
So, anyways, just thought I'd toss out some options for you to consider and review over the next 5-6 months.