I think your best approach is to do this:
- Convert to Mobi using Calibre
- Use the utilities on the mobi subforum - I believe it's mobiunpack, to convert the mobi to Mobipocket Creator's native format.
- Do your final edits using Mobipocket Creator.
You should be able to get blockquotes working if you follow the steps I outlined before, they're working for me. A bugfix just went in for scenarios where the 'ignore margins' setting is enabled, but it works fine without ignore margins today.
Superscript may be a bug, I don't know how you've defined your css for that, but in general mobi doesn't appear to allow much in the way of formatting superscript. Check this bug for more details:
If you've defined it in epub css matching those parameters then a fix will likely be in the next release.
The font issue is most likely a bug, but we'll need the details on how you defined it in the CSS.