i have been on several long hikes (40-50mi) on the AT as well. What part of the trail are you going on??
i would reccommend hiking each night after school or work. if you have them, find the biggest hill you can, and hike it 2 or 3 times. if you only have one or two small ones, hike them one way, then turn around and huke them back. jog as much as possible. lung stamina is THE MOST important thing. as you climb, air gets thinner. it may not seem like you really are hiking that hard, but things get really tiring realy quick. getting your hips in shape would probably be next (as your pack SHOULD NOT rest on your shoulders).
once you feel you are in shape (or getting there), get in as many hiking trips as you can. im not talking about 2 or 3 miles, put in 20 or 25mi in ONE DAY. It will tire you out, but it gives you a good work out. do this as often as possible.
if ya got any more ??'s, feel free to ask me. i'll try to help out (although it may not be "professional" help

)