I wouldn't worry so much about the D40 lens limitations. Apart from the 50mm f1.8 prime lens, there are no really essential lenses in the Nikon lineup that a beginning shooter would want that aren't AF-S. And manually focusing my 50mm f1.8 has not been a limitation so far.

You can pick up plenty of used AF-S lenses at www.keh.com. Here are some examples.

http://www.keh.com/OnLineStore/Produ...W=nikon%20af-s

AF-S image-stabilized 105mm macro (pricey, but a nice lens)

http://www.keh.com/OnLineStore/Produ...W=nikon%20af-s

AF-S 24-120mm with image stabilization.

http://www.keh.com/OnLineStore/Produ...W=nikon%20af-s

AF-S 70-300mm with image stablization.