I'm not exactly sure what all your issues are.
You are correct that this plugin is not designed to remove series values - it is for adding/renaming series, not removing items from a series. That is intentional given it is just as easy to blank the series cell in the library view (or use the bulk edit dialog). I would have thought that removing a series from a book would be one of the least used functions. So I don't see anything changing in that regard.
As for the editing an existing series name, I can't replicate the behaviour you describe. Certainly if I have a "Harry Potter" series, I remove "Harry" from the series name in the combo box then straight away the new series name column changes and when I click ok "Potter" is the new series name. If you can replicate some other issue with this and detail the exact steps then I will happily take a look.
As for your last issue with the custom column, again without some details there is nothing I can do. No-one else has reported any issues with this plugin but that is not to say there might not be an issue there, particularly since secondary series custom columns would be pretty rare in the user base.