1. If the "little stones" are white or whitish, look very porous and crumble very easily, they are most likely what people call "sponge rock"; or more accurately they are called perlite.
The simplest description of perlite is that it is a rock that is made up of volcanic glass and the pores are made from gases during the formation of the material.
In horticulture, people love using perlite because it is lightweight, does not degrade as quickly as organic matter does, and because it is porous, it has water retentive properties as well as provides some air circulation to the plants roots.
2. "Crumbled bark" is no good for an orchid that grows on living trees. The debris from the crumbling bark will suffocate the roots by severely reducing the amount of air that gets to the orchid's roots and by retaining too much water (too much water = drowning the roots = suffocation).
Repotting was really a great idea. Good job!
3. The yellowing leaves may be physical signs of damage done to the plant long before you obtained it.
4. Reducing the pot size may be another thing that might be needed, particularly if root system was severely damaged.
5. Check the condition of the roots in the pot, don't just pay attention to the "aerial roots".
6. Let your plant dry out a bit between waterings.
7. I highly recommend understanding how a Phalaenopsis really grows in nature. I think it will help solve some basic issues with problems associated with growing Phals.
Any further questions, just ask.