Hello and welcome to the OB.
Could you possibly post a picture or two of your plant, I'm not clear on your question.
By "stem" are you refering to the base of the plant that all leaves originate from or are you refering to the flower spike?
If the base of your plant is wet and soggy, it has probably been overwatered or water has been allowed to stand in the crown of the plant. I am sorry, but I believe your plant is probably done for.
Joann
I can see your photos.... Regarding the spike on the phal, I would trim the end of the spike slightly if it is not completely dry, just into healthy tissue using a sterile cutting tool. The cut can air dry. I can see on your photo that the spike has started to branch, which will lead to new buds and flowers.
Knowing nothing about your oncidium problem I would recommend at least quarantining the plant first and foremost. Are the bumps raised (possible scale), or sunken (fungal or bacterial problem)? Hopefully someone else will be able to assist you with this plant.