I will be eternally grateful to anyone who can help me solve this problem.
The thing I use my kindle for most is manga. I use the wonderful Kindle Comic Converter to convert CBR's and whatnot to mobi/epub. Only problem is the metadata. KCC will use either the filename or comicrack data to form its metadata, some of which can be edited, but to a limited extent. Also, calibre and every other app will edit some surface metadata so for instance I can have the title of a book be "Sundome No. 1" in calibre, but if you view the metadata in calibre or on the kindle, it will say "Sundome V1" because that's what KCC entered.
If you manually edit the metadata in calibre or any other app, it edits that "surface" title, but not the title that's actually showing up on the kindle. I have noted that the metadata and "header information" seem to be different and that's where the issue is. The header will say "sundome No. 1" and the metadata says "sundome V1"
I apologized if i explained this badly. I can take and post screenshots if this is too confusing on its own. But I really need help with this. It's driving me nuts.
Thank you all!

As you can see, the list view title and the metadata editor show the same thing. But when viewing the actual metadata in the calibre reader or on the kindle, I get the title stored in the header (which I have no clue how to edit)