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I don't know if that will help with reflowable ePub 3.0, but you could do your own font—at the minimum one glyph—with InDesign by using this script by Jongware and Marc Autret:
There is a free demo version where you are able to save an OTF with one glyph only.
So at least you would be able to test that scenario.
Most of egyptian transcription characters are found in windows times new roman.
If you want to set inline character height acording to character height, there is a way. I cannot appoint you to the exact resource, but it is doable. It includes fiddling with content.opf file and css file.
And it is working only with apple ibooks reader. For most other readers you must use inline graph as div element. And then edit css accordingly.
Since your responses, I found fonts that do the job. One is called, JSesh for the hieroglyphs and another is a series of fonts called, Inscribe. Both work well, but I ran into another snag. Many eReaders don't support either of these so they'll either insert their own font or leave a square block if it can't resolve it. Making my own font won't work, but thanks for the idea, Uwe.
Times NR is a viable option for the transliteration since it's widely supported, but I'm waiting to hear back from my publisher if it's supported on the various eReaders our book would be read on. If it is, then I have the transliteration problem solved, thanks to Ants' suggestion.
For the hieroglyphs, I was thinking of two possibilities:
Convert the 15pt JSesh font to outlines and convert to PNG, upon export. Hopefully they still retain enough detail for legibility.
Make SVGs from the outlines. I haven't done this before so I'm still researching if this is even an option.
Have either of you worked with SVG in ePUB 3 reflowable? If so, can you point me to a source on how to put these into an ePUB? My guess is I'd have to crack open the book and swap out every instance of PNG with an SVG. It would probably involve manually editing the content.opt too to include them ??
This seems rather dodgy, what happens if the reader changes the font or wants to use night reading mode?
What about coming at it from a different direction and have a note number or common symbol on these words that references a page where all the unusual letter forms are referenced. Not elegant but it might be easier to produce and safer. Just a thought!
You must include font with your epub and tell reader software to use included fonts. I recommend everyone to set their ereaders to use included fons and original layout. Also there may be problems with font obfuscation. Some older models do not support IDPF method. Turn it off for your fonts.
There is no big difference between SVG and png. SVG will scale more smoothly, but your sizing problems will remain. I havent tested recently, but some times ago there were the issues with epubchech in epubs containing SVG graphics.
Sorry for the delay in getting back. My publisher got back to me and confirmed that iBooks does support the JSesh font for hieroglyphs, so I'm going to leave it in and not convert to an image. The same holds true for Times New Roman for the transliterations.
The only other hurdle I have is how to stack 2 hieroglyphs which occurs in several places in the book. I'm making a new post for this one.
Thanks to everybody for their input.