I can right click custom markers to select them, but have yet been unable to alter or remove them afterwards?
Anyway, time for a next run

. At this rate I'm only done after 40 hours XD (not that I'm complaining ;))
EDIT, some screenshots added to Steam to show some of the issues
mentioned (after seeing someone do that in another thread).
Broken Initiative UI element
Upper/lower levels appear on world map - bug