Alan
In those times, it was usual to create custom fonts, and associate keyboard layouts to such custom fonts. Now, it is highly recommended (to not say it is mandatory) to use unicode fonts. First of all, there are some very good free fonts for linguistic or dialectal texts (e.g. Gentium) or commercial, but not expensive fonts (e.g. Aphabetum, Juan José Marcos). There are also good keylayouts, e.g. IPA Unicode or, if you allow, my US Academic (I should not be lazy and update it a little bit).
Cyrillic, including extended Cyrillic and Old church Slavonic are also available in good free fonts, e.g. Dilyana (for OCS), while Extended Cyrillic (for noting non-Slavic languages of the former Soviet Union) is available in many current fonts.
If you have your own fonts, I would therefore suggest to ‘unicodify’ them, so that you may come up with the times. You complicate your life too much if you choose another way. But, of course, the choice is yours.