Help with root rot on Phal

[cassie.g]

Hello!

I got the phal in question back in March. I repotted it right away into a glazed ceramic orchid pot in bark and cut back the rotting roots. Since then, it's seemed to do pretty well. It's putting out a new leaf which is a little over half the size of the others as of today, and has lots of new roots. It's also putting out what I'm pretty sure is a root up where a spike would come out.

However, I noticed some rot today on it's roots going into the media that I don't think was there before. The aerial roots seem okay, but I'm not sure about the other ones. I cut off the rotting roots that I could see without pulling the plant out of the pot (I'm not sure if that was the best idea, but that's what happened).

I'm wondering if anyone could clue me into what caused this and what I should do. I have a feeling it's due to overwatering (I was watering around every 3 days). I started using the skewer method recently so hopefully that will help my watering "schedule." Should I wait to repot it and risk that the roots are continuing to rot, or should I repot now (probably into a clear pot) even though it's only been a few months?

Thanks in advance.

---Also---

Some of the aerials roots have little touches of brown on them (I can post a picture tomorrow). They seem to be fine, but I'm not sure. Also, the root tips occasionally turn partially brownish. Could this also be attributed to overwatering? I also read that salt buildup could cause this.