CK....I'm new to this forum, but have hiked many a mile and when I read your OP, my first thought was "You're humpin' too much s**t troop!" 39 - 40 lbs is waaay too heavy to be packing through the mountains in any weather. I'm +1 on all who said ditch the chair, bear vault, goal zero solar power charger, 32oz. Nalgene bottles, and the wind screen ( you can't use one with a canister stove unless the can sits outside the windscreen). Get rid of the Goal Zero and carry extra batteries. Their lighter and the GZ doesn't really work that well when it isn't consistently exposed to sunshine. (I know, I have one, and it's never worked as glowingly as the GZ folks hype it to). I'd keep one of Duke's bowls. Instead of the 32oz. Nalgenes, I'd get a couple of 1L Smartwater (or equivalent) bottles, and/or a 2L water bladder. You can use the Smartwaters not only for drinking water on the trail, but also in camp, and they weigh a lot less than the Nalgenes do. The bladder will afford you fewer water stops, as well as filtered water (presuming you used your filter to fill it) once you've stopped to camp.
I know you're on a limited budget, but if you save some $$ and look on Ebay you can find far lighter 2 person tents than that OT behemoth. In fact, I've got a 1 person tent that weighs only 3lbs and you could shelter Duke if need be by a $10 5x7 tarp (Wally World camping section). I don't see if you're using trekking poles (also not very $$ @ Wally World) which can be used to help setup the tarp. Look online and get some Aloksak Opsacs. These are odor barrier bags that come in various sizes and alleviate the bear canister need. You can replace the chair with any of these (all of which are lighter than the Crazy Creek):
http://www.rei.com/product/765283/rei-trail-stool http://www.rei.com/product/845302/rei-sit-pad http://www.rei.com/product/829881/th...est-z-seat-pad http://www.rei.com/product/829895/th...kker-chair-kit (this one is designed to use with your sleep pad as its support)
NEVER EVER REDUCE THE AMOUNT OF FOOD YOU'RE TAKING UNLESS STOPPING FOR RESUPPLY. I can't emphasize that enough. Always carry one meal more than you htink you're going to need. There are tons of available resources (right here on this forum I'm sure) that can tell you where the shelters are and where you can resupply. Max Patch is right: Duke will eat way more on the trail. I know you've been training, but as has been said, walking in the relatively flat, humid, warm climate and terrain of FL is way different once you've gotten to the AT and you're starting out on top (mostly) of a mountain. It's a whole lot of up and down. (Duke won't need the booties either).
One last thing.....invest in some emergency duct tape (made by SOL or McNett) and a little travel sewing kit. Crap happens and you can fix almost anything with duct tape.
I don't think you've made any kind of mistake in your training. Just in your gear selection. If finances don't allow it, then you've got to go with what you've got. Just keep in mind that ~40 pounds is going to seem a chore after about the first day and a half of mountain trail walking.
Another thing that comes to mind is have you seam sealed your tent? Did you get the Frogg Toggs ultralite rain suit? If so, buy the poncho as well. Leave the pack cover at home. Not that there's anything wrong with a pack cover. They're great if you're going to use them at night to cover the pack, but when it rains and you're wearing the pack, water will run down the straps and onto/into your pack. The poncho will cover both you and your pack. (of course you could always go with one of these : http://www.golite.com/Poncho-Tarp-P8...nt=22056985244
)
So, take all this for what it's worth, use what you want, ignore the rest and have a good hike! Let us know how you're doing when you're on the trail.