Your issue with PDFs may (only may) be related to Calibre.
The reason I suggest this is that my tool for producing RTFs can also create PDFs, so I got my colleague to test a sample I knocked up. He transferred it via email over wireless (no Calibre involvement) and upon arrival the metadata was fully intact for Title and Author. That, combined with your comment about the issue with Calibre's copy, is a little suggestive to my mind.
That said, even PDF isn't perfect on the Kindle.
I don't care about the scaling as my tool creates them paginated them for a small screen and uses a large font, so scaling is not needed on any e-reader I have tried, including both Sony and Kindle. However the Kindle totally ignored my table of contents, unlike Acrobat Reader on the laptop and my Sony PRS505, both of which understood it perfectly and offered me suitable navigation options.