Dont think that there is anymore production of D40x unless you are considering 2nd hand market units.....
And yes, major difference between D60 vs D40 is megapixels and also sensor clean features.... I have a 10.2mp D40x and a 6.3mp D70. My only complaint of lower megapixel is limited cropping capability that I can do.
Never did try the sensor clean feature but I am fine living without it so far..... My D70 is at 19K shutter count and I sent it to NSC once in these pastg 5 years for general servicing and cleaning. My D40x is 15 months old and has not suffered from any major dust on sensor issue as well. About 10K shutter count at present.