I started with a D40, 18-55, and 55-200 VR and it makes for a very light, compact, versatile kit. If low light performance bothers you the most, I'd suggest either a tripod if most of your subjects are stationary or a fast prime if your subjects are more mobile. I've never used the 35/1.8 DX recommended above, opting instead to go the manual focus route with a 50/1.8 Series E. I ended up getting sucked in by manual focus glass and the two kits lenses are actually the only autofocus ones I own. I wouldn't say a flash is necessary, even now that I have a couple I don't use them all that often, preferring a fast prime and natural light in most instances, YMMV. When you get one make sure it can tilt or swivel so you can bounce it.
When you get a tripod, get the little $20 IR remote too. Its super handy, tiny, and about the cheapest accessory you can buy for the camera :D. Don't skimp on a tripod either. I never imagined I'd be looking at a Mamiya RB67 when I bought my legs but I'm glad I went a little overboard with them. If I do get the RB, I'm going to need a new head because I did skimp there. Live and learn...
As far as reading, Understanding Exposure seems to be the standard for, well, understanding exposure and is a great first book. I really the The Photographer's Eye by Michael Freeman and many of Galen Rowell's books as well. But the best way to learn is to put you camera in Manual mode and start figuring out for yourself how different combinations of shutter speed, aperture, and ISO change the image. Learn to read the histogram and figure out when your meter is lying to you and you'll be off to a great start!