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Calibre will help convert mobi to epub or the reverse. k2pdfopt can help convert newer pdfs to older standards. Ghostscript can too, but its transparency-handling is incompatible with the Mac and Kindle.
I'm not sure what would support your password options.
I also have a ton of trouble with touchscreens, and use a Kindle Dx. It's good for most articles, if I use either k2pdfopt or Ghostscript, depending. It's good for scanned pdfs if I run them through k2pdfopt. It really falls short with some graphically-demanding pdf-born-pdfs either way. Because of that, and because of the library management headaches of converting every pdf to multiple formats, I am wondering if another reader might be better.
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