I live in the area. its not worth going to the caloosahatchee trail right now (unless you like mud riding), you'd be better off with a swamp buggy. The North Port trail will be damp but not flooded. unless you're into wooden structures I wouldnt go there as the trail is basicaly linear and Naples is really close to markham park and the trails there are much better. If you got a road bike bring that instead.
Theres also the trek bicycle store of naples, and they've got a tech that spends quite a bit of time on a mountain bike. hes a young guy, like 20, and always wears an apron, pay him a visit.