Yes, you can put whatever DRM-free content you like on your Kinlde (as long as the Kindle supports the format).
Amazon has no say in what you put on your Kindle. Amazon does not check the files on your Kindle and/or take any action based on that. Whispernet is for syncing Amazon-purchased books and will not affect your other books in any way.
The Kindle has a rather limited range of supported formats though. Basically PDF and MOBI. Files not bought from Amazon will only work if they are DRM-free, which is easy to achieve (and in most places legal assuming you acquired the file legally in the first place).
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