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Emacs has the commands iso-iso2tex and iso-tex2iso that work very well, except it doesn't convert single commands like \OE to Œ.
Don't redefine \r as this is the 'ring' used over 'å'.
You may want to consult Dr. David J. Griffiths's web page at http://academic.reed.edu/physics/faculty/griffiths.html. At the bottom of the page he provides a link "To create script-r in TeX:" http://academic.reed.edu/physics/faculty/griffiths/script_r.zip
I think you should use biblatex and biber, not bibtex: the main reasons being that 1) biber understands utf8 encoding, so that accented characters, greek, arabic or chinese will not be a problem; 2) biblatex is much easier to customise (if necessary) than bibtex, as it uses latex-style commands, unlike bibtex, which has a language of its own that uses ...
The package selinput was not yet mentioned. Because I found good answers regarding its use on other places in TeX.SX let me first link to them: Heiko Oberdiek (author of selinput): The input encoding depends on the editor that is used to write the TeX file … If the user is troubled to find the right encoding, then package selinput can help, … ...
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