Apparently ZUN has stated several times that the PC-98 series isn't actually canon to the windows series (the wiki actually has links to those various interviews). Thus any reference to a PC-98 game in the Windows games is more like a mythology gag than a confirmation that the entire PC-98 series is canon to it. Of course, that doesn't mean PC-98 characters or locations can't "return". If anything, it gives more freedom for them to return. It's just a question of whether or not ZUN would want them to (many of them didn't because he didn't feel very comfortable with them in the windows version of the Touhou story. Some like Rikako really wouldn't make much sense after several stories in the windows game like Silent SInner in Blue, etc, have taken place)
In this regards, it is highly likely that several Windows characters are revisions of certain PC-98 characters. Meiling is probably a revision of Orange (in fact, their battle dialogues are VERY similar) and Kaguya is likely a revision of Kotohime (both are rabbit princesses and collectors)
I do sincerely believe that Mima is the current god residing in the Hakurei shrine. Because given the situation (of the god being angry at a lack of faith and things to the point where no one remembers her name), that's hilarious.
I like Yumemi a lot. However, I think Maribel's stories are basically a revision of Yumemi's themes. Yumemi is a teacher of a university in a world where all energy has been unified and magic is the one thing left unexplained. Magical Astronomy is basically the story of a university girl in a world that has unified all forms of energy discovering one that hasn't been unified yet and being declared a magician (magic) for it in the end.
...it'd be cool if Yumemi was one of Maribel's professors, though.
Honestly not sure I'd see the point of most PC-98 characters reappearing in the windows game. A lot of them were very undeveloped and really wouldn't have a unique niche now that several Windows characters are there (we already have poltergeists, maids, vampires, etc)