Phalaenopsis: leaf disease? Wet roots?

[LKint]

My supermarket phalaenopsis bloomed last year in the summer and I left it in the bark mix and aerated plastic pot within an undrained ceramic. [I forgot to take it out!] New flower spikes appeared over the fall and I moved it from behind a lacy curtain by the window to a table 5' from the window with some partial full afternoon sun in the winter. Yesterday I did my weekly light watering [without first checking for dampness] with a dilute "Miracal Grow". Today I noticed one of the three flowers only about a week old had dropped.
I inspected the plant and found a leaf with a major blemish and a second leaf with a blemish starting. I cut out the two bad sections. First is that the correct action, or should whole diseased leaves be cut off?
The photo shows the damages. Can you diagnose?
Then I saw that the roots had driven down through the plastic pot's bottom drainage holes and were in 1/2" of water. When I cut off those bottom roots I could lift the plant out for repotting and found most of the bottom 2" of "stem" and roots were rotting in the damp bark. I sawed off the bottom 2" and some other rotted roots and repotted in a wider aerated pot in the sphagnum moss mix I bought. Is the plant on its way out after such radical surgery? If not, what care is needed during this recovery stage. [It has two flower stalks with buds.]