Transcription/transliteration of the traditional pronunciations

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Yemenite Hebrew has both [θ] and [ð] while a Greek sub-tradition has only [ð]. Would it make sense to use th for [θ] and dh for [ð] in the former case but th for [ð] in the latter (going by English orthography), or would it cause too much confusion when putting them next to each other? Would it make more sense to use dh for [ð] when discussing the Greek sub-tradition by itself?

How should I distinguish e.g. [sh] from [ʃ]? How should I maintain uniformity with traditions with no [ʃ] (e.g. some Lithuanians would pronounce שָׁנָתְהוּ [ʃonoshu] while others would say [sonoshu])? Is maintaining that uniformity necessary when putting the transliterations next to each other?

[Drink]

Yemenite Hebrew has both [θ] and [ð] while a Greek sub-tradition has only [ð]. Would it make sense to use th for [θ] and dh for [ð] in the former case but th for [ð] in the latter (going by English orthography), or would it cause too much confusion when putting them next to each other? Would it make more sense to use dh for [ð] when discussing the Greek sub-tradition by itself?

It would certainly cause too much confusion. It would cause confusion even if you discussion that one Greek sub-tradition by itself. Please do not do that. Use "dh".

How should I distinguish e.g. [sh] from [ʃ]? How should I maintain uniformity with traditions with no [ʃ] (e.g. some Lithuanians would pronounce שָׁנָתְהוּ [ʃonoshu] while others would say [sonoshu])? Is maintaining that uniformity necessary when putting the transliterations next to each other?

This is why linguists normally do not prefer to use digraphs. However, those that do use digraphs, will find a way to break up the digraph when it's not meant to be a digraph, for example with a hyphen: [shonos-hu] [sonos-hu].

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Would something like this work?

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I want it to look as much like standard English/European orthography as possible and to use as few diacritics as possible. Where two sounds have the same transcription, they will always be distinguishable by context (they're either allophones or distinguishable by the tradition in question, which will always be clearly indicated). What should I do with ch? Shoud I use it for [x], [tʃ], or neither? Since I'm trying to emulate standard English/European orthography, I feel like I should use it for something.

For the diphthongs that occur in Ashkenazi Hebrew, I will refer to our previous discussion:
https://forum.unilang.org/viewtopic.php?f=34&t=56397

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I also want to represent allophones with the same letters as much as possible (so, perhaps g for [ɢ] in those cases where it's an allophone of /ɡ/, either b or v for [β] depening on whether it's an allophone of /b/ or /v/, u for [y] and e for [ə] if allophonic, maybe something different with [ɕ] [tɕ] [ʑ]) and, as stated, use as few diacritics as possible. Should I represent all of those sounds separately? I do also want uniformity. What should I do?