Beginner repot of a repot after a fungus outbreak

[LisaK]

I'm hoping I can post my repot photos here, since I couldn't add them to my thread in the forum of Pests & Diseases.
In short, I received two mini phals as gifts about 6 months ago and everything was going great. They probably needed to be repotted two months ago but I have been recovering from surgery and pushed my luck. I'm a beginner and I saw these spots appear, after a lot of reading online etc. I think I had maybe mites that caused bacteria to grow under the leaves. Someone on the board in 2008 had pictures just like mine wondering what it was. I heard about neem oil and cinnamon and have now learned the way I used them was not helpful to me. After repotting 2 weeks ago I saw big long fungus grow quickly. This time I repotted by only washing in pure water, cutting off soft roots with a sterilized pair of cuticle scissors. And placing them in the smallest orchid cups I could find online 2x2 clear plastic bottom slatted ones and used the tiniest pieces of bark. When I got them they came in sphagnum moss in a 2 inch wide, 3 inch long container. When I repotted two weeks ago they had so many long roots I repotted into a 2 3/4 x 3 inch tall clear slatted pot that I put inside a decorative pot. This time I went even smaller than ever since I lost so many of the roots so fast. Praying for a great outcome and that the darker one's spike makes it to bloom! Thank you everyone for your continued support! I'm open if anyone thinks of anything else.