1. Editing window. Clickable tags in note preview are in separate request.
2. Good question. I guess having some special syntax for tag references it should be easy to rename references automatically.
3. I think simple clicking. But in theory all the modifiers can be supported here, too.
4. IMO the second variant is more feasible.

I guess you should vote here: http://roadmap.cintanotes.com/feedback/3385-search/

Can be implemented without any problem, but as a separate request:
http://roadmap.cintanotes.com/feedback/7340-backup-now-command/

Well I see no problem in autosaving drafts in Recycle bin and moving them out of there on "OK" press. Or is there some inherent problem with this approach?

Why only 2 and not all of them, could you elaborate please?