I was a bit hit or miss with PDFs too at first.
Then Amazon gave me an email address to send documents to and they are automatically translated to a kindle format. I didn't ask for the email address, it just came up after an update to my iPad version of kindle viewer. Although of course it works fine on my actual kindle machine too.
Presumably if you have an Amazon account, you will be able in your settings to see your email address for sending docs to? They then appear as if you had bought them in your archive.
Works for me.