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Good day, Katrina:
For the first line of your file GreekPhiAfter-1Subscript.jpg, I would use the following braille:
[simbraille].f^-1 .k ,f;-2"+,f;-1".f .k -#1+.f[/simbraille]
which is the same as your first suggestion.
The portion you indicated with underlining does not require a multipurpose indicator after the baseline indicator. (In your second line of simbraille, did you mean for the first underlined braille cell to be a dot 5, which is the multipurpose indicator?)
I believe that the simbraille you suggest for the first two lines of GreekAfterSubscripts.jpg is correct.
I'm not sure that Rule V, section 32 is relevant to this issue, because it deals with typeforms, and this issue deals with the Greek alphabet.
I would look to Nemeth Rule XIII for guidance on superscripts and subscripts and to Nemeth Rule IV for guidance on Greek (and other language) alphabets.
Please do let me know if I did not completely answer your multi-part question or if you need more information.
Thank you for your time,