Let's see if I can help -
Question 1 - key signatures. The braille reader should just be required to indicate the signatures as they read them in braille.
Question 5 - adding accidentals. You could braille each whole note with a blank cell in between them, giving space to mark where a flat or sharp would go. I don't think adding lines is necessary.
Boxes and circles - I would make them distinct, for sure. For boxes I usually use music brackets around the enclosed notes in all parts. Circles would be fine with music parentheses. Use word sign expressions with the letters and numbers of the boxes/circles in all parts before the brackets/parentheses.
In exams and theory books like these where there is a lot of visual stuff going on, include a transcriber's note before everything that might not read easily. So before the example for questions 20-28, write a TN that says something to the effect of "In print, lettered boxes and numbered circles enclose different notes and chords. In braille, boxes are represented by music brackets and circles by music parentheses. Letters and numbers precede each boxed or circled note or chord in all parts."
(Luckily, you don't have any overlapping boxes or circles here! That gets messy, for sure!)
Hope that helps. Let me know if you have any more questions.