Repotting Zygosepalum

[Judi]

I boughtg a Zygo in bloom several yaars ago. It has grown but I think it needs help. I think I should repot it; some of the pseudobulbs are shriveling and are getting softer--is this common for old pseudobulbs or do I have a problem here ? It had new growth that rotted--I think it was touching the pot--I cut it and the plant dried and recovered nicely at the cut. Anyway the remaining new growth looks healthy but is mostly growing way above the medium, also the leaves have black spots on them. How do I repot it ? Do I keep the old leaves and pseudobulbs? Is it normal for the normal growth to be above the medium or should I plant it deeper???? I am attaching some pictures, please help!