Hi, Shawn, and welcome!
I haven't used gaiters in a while, but they are a good idea when backpacking ... I prefer the ones that just cover the ankle area rather than all the way up the shin. Check the CampMor catalog or their online store. I still have a pair of these around:
http://www.campmor.com/outdoor/gear/Product___14235I can't speak to hiking with dogs, other than it would be smart to stay out of swamps with them, and only Eglin outright bans dogs on their part of the Florida Trail. But section hiking, that's what I've been doing, and it's how I wrote The Florida Trail: The Official Guide (with help from Deb Blick on maps and places I didn't get to hike). The book has gone out of print and I will be out hiking this season to update it. You can find used copies cheap through Amazon.com (wish I'd stocked up on it!). I broke the trail into logical sections from major trailhead to major trailhead that made sense for section hikers. You can sit down with the full set of FT maps and figure out the same thing.
Cheers, Sandra Friend