Flags: Get your Q and Bahamas here and pick up the rest as you need them (and cheaper!) along the way. Every island has someone selling them for 10-15 bucks.
Keep an eye on the above for listings, Check E-bay, call around to ICOM installers to see if they have removed/refurbished units for sale.
Other stuff: We've been treating this as a reasonably short, one way trip down island to Dominica so I don't think you need to go crazy with battery systems/inverters/fancy stuff etc. as you would for an extended cruise.
The one thing I would emphasize about the trip once you have the above prep done is that it is TO WINDWARD for much of the way into larger seas and heavier average winds than we see here on the east coast. You will be motoring much of the way using your mainsail for steadying. Critical to your happiness and success will be:
1. Having an engine that is in tip top running condition. Transmission too!
2. Having all reasonable spares to repair that engine...not just belts and hoses and filters.
3. Having clean fuel tanks that will not clog you up when you hit rough weather.
4. Putting clean fuel into the engine along the way. (BAJA FILTER or similar)
There is little in the way of service and nothing in the way of parts available once you get to the southern bahamas and until Puerto Rico. Generally other cruisers or a local guy can help you out with repairs if you can't do something yourself, but they can't help you at sea if the engine fails and they can't help you in port if the needed part isn't in your kit.
The good news is that there are no IED's along the way to worry about! ....and you will see some beautiful places and meet some great people along the way!