Newbie Phal / Dendrobium Re-potting Questions

[mmorehead]

I noticed that some of my phals had black or dark brown roots. I use the clear containers and monitor them constantly. One phal had just lost all its blooms, and I decided to go ahead and re-pot it. Upon examining the underneath, I noticed that some of the roots coming out of the rhizome were brown, some mushy, with little white fibers. Others were off-white with black spots. But some of these dead root fibers contained new growths of healthy, thick green roots. I accidentally cut one of the brown roots from the rhizome that contained three, very long and healthy green roots sprouting from it toward the bottom. I fear that it was not the proper thing to do. So, before I go cutting any further, I just wanted to make sure, being a newbie at this, that I am doing the everything correctly. Any advice would be greatly appreciated.

Also, I bought a Dendrobioum Phalaenopsis from a local grocery store. It was packed with sphagmum moss, and I noticed today that one of the leaves had black spots on it. So, I removed the sphagmum and noticed how much moisture this den had been retaining. There were nothing but brown roots, with only a mere few white-ish/green roots at the rhizome. Do I cut all the brown roots, even though they aren't "mushy"? If I do, it will only leave a two or three very small pale green roots to work with. Also, the leave that had the black spots, I went ahead and pulled it off, just in case it was something that could spread.

Any advice you could give this newbie would be most greatly appreciated. I've read so many things in regard to re-potting and cutting roots, but I want to be sure I'm doing it properly so that these beautiful orchids can thrive. And thank you for your patience. I feel that I may have done some no-no's in this re-potting process.