Hi Fred. Thank you for your questions, and for sending us to the Provisional Guidance document for answers.
Yes, "freestanding" includes numbers or letters with punctuation. The example on page 2 of the Guidance shows a UEB number 3 and a UEB letter n with a following period. It is not really necessary to include this information in a transcriber's note, unless your agency or a teacher has asked for it.
I like your solution for rendering the numbered boxes. The numbers are not showing up in your scan, but I get the idea. Regarding the answer choices, I find the terminology "blank section" confusing, but I see that is what it says in the print copy. I'm guessing this test is printed from an online or digital format, which often makes less sense on paper. (The online test-taker probably clicks on their answer choice and it probably will pop into the box in the sentence, I'm guessing.) Regardless, your task is to provide the information clearly to the student. This is really a question for the Braille Formats folks, but I would suggest moving the answer choices to follow each blank in the question, similar to Example 10-19 in Braille Formats. The answer choices are put in parentheses, and you will need to separate the choices somehow. I suggest a spaced slash. This change absolutely requires a transcriber's note. See the attached BRF file for my solution.
I see you are using a square (box) symbol for the scoring numbers. (I assume there is a little box to the left of each slash? It is not showing up in the scan image.) I suggest using UEB there as well, transcribing an underscore instead of a box.