I wouldn't be contemplating a South Florida and Bahamas sojourn in September and October - it might be the end of the hurricane season but it's by far the most active time. That might just me being overly cautious, but I've encountered enough hurricanes whilst making my way south from the Bay to the Keys to have great respect for them.
I'd head straight up to the Bay planning on going inside all the way with a chance that you'll have to hole up at some point to avoid a storm. Remember that going offshore you'll get large swells if there is hurricane activity even very far away, so if you see a window that will let you out for a few days offshore, just check that there is no unusual swell being reported. I once went offshore at Beaufort, heading south, and found an enormous swell running with only 15k of breeze - it was caused by two hurricanes passing way offshore.