Having gone from a D40 to a D80 (still have the D40 though) I wouldn't try to argue that the D90 isn't an upgrade from the D60 since it is, if only by a little bit to some people. The external buttons for basic functions alone might be worth the upgrade (plus there's more customization and you can AF older lenses etc.).
As for the lens question, unless you tend to shoot mostly at or around that 50mm point with your 50mm lens or kit lens, you probably won't be happy with just the 50mm lens. I personally (if I were willing to get rid of a camera other than by "lending" it to a friend or relative) would sell the D60 with kit lens and buy the D90 with the 18-105VR, since you might have a better time selling the D60 with the lens rather than without, even though you might not get much more for it plus, based on what I've read, the 18-105VR seems to be a better lens than the 18-55VR and the longer zoom would be great in many situations where the 18-55 runs short (can't count the number of times that's happened). You could also sell the 50/1.4 but I wouldn't since it's just too good a lens to get rid of unless you never use it (and if it were the 50/1.8, you wouldn't get much back for it anyway).