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You first can check if the font has the diacritics you need. Some use FontForge, but that is perhaps quite heavy. However, be aware that most fonts are not allowed to be embedded. One font that is allowed, is Charis Sil. It is also quite complete, although on the heavy side.
If you open your ePUB in Sigil or the Calibre Editor (I have a love/hate relationship with the Calibre editor with regards to fonts), you can replace all the fonts and adapt the stylesheet to ensure the fonts are used.
Subsetting of the fonts can be done with the Calibre Editor. My own program FontShrinker can also subset all the fonts in an ePUB, but you need the current version that is not released yet. The older version works differently and less friendly. I hope to release that one tonight, depending on some testing from one of the residents on this forum.
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