Shawn, I would suggest purchasing AT maps from the ATC, Appalachian Trail Conservancy. You can also buy some AT maps(with Guide books) at REI or local outfitters. The ATC has made a series of Maps of the entire AT. From Maine (Maryland) to Georgia. Of course the emphasis of the maps are on the AT, however on these maps you will be able to see side roads, secondary roads, forest service roads, and major highways that run close to or cross the AT. You can also visit Google Maps, and find AT Shelters on the AT. Zoom in along the trail and you will also see roads in which to bicycle. Bicycles themselves are not allowed on the AT.
I see that you rode the Pacific Coastal Bike Route. There is an Atlantic Coast Trail, but not along the AT. You could catch it around Norristown, PA and ride all the way to Key West, FL. I would also suggest the TransAmerica Trail that runs from Yorktown, VA to Astoria, OR. 4,000 miles in about 3 months of pedaling. These routes are already laid out, they have maps and places to stay. Visit Adventure Cycling Association for more details. Hope this helps.
_Bilko_