There are three points in the Park where you can shop for the usual gift shop goodies as well as some more specific park items.
Firstly, the Painted Desert Visitors Centre which has the best selection of National Park products, including the opportunity to purchase your own specimen of petrified wood.
Secondly, the Painted Desert Inn which has a variety of photo exhibits and a related book store.
Finally, there is the Rainbow Forest Museum which has the usual gift shop items.
If you are going to buy anything, I strongly suggest doing so at the Painted Desert Visitor centre as it has the widest range.
At the south entrance to the park you'll find a large souvenir shop that offers all the rocks, fossils & petrified wood you could possibly want. They also have an extensive selection of "glass artifacts', which are colorful rock-like chunks of glass, refuse from the glass bottle manufacturing industry. There's a fountain built from some of these glass artifacts, quite interesting to see.
The town of Holbrook is rock-fanciers' paradise too, stop in if you're looking for the ultimate deal. Oh, and consider staying overnight at one of the most famous Route 66 stops, the Wigwam Hotel, it's a hoot!