Agree with John. It would hard to buy a new D40 and D90.
D7000 1)better resolution; 2)better high ISO preformance; 3)better focus module. Both D90 and D7000 have buildin AF screw. You can AF 50 1.4d.
Here is in depth comparsion D7000 vs D90 from dpreview:
http://www.dpreview.com/products/compare/side-by-side?products=nikon_d90&products=nikon_d7000