Bonsais are pretty hardy. I wouldn't worry too much about removing those stones. You can move the soil around as long as you don't rip up the roots too badly. The tree needs to be completely repotted in new dirt ever two years anyway. The biggest thing to remember about bonsais is never to trim them from the top, only from the bottom and sides of the limbs. Keep it no wider than the pot it's in. This will keep them from becoming root bound. 

My father raises a lot of bonsais. Feel free to email me if you have more questions: bloodcrossed@gmail.com

~Tara