Susan,
Thank you for the questions. I apologize for the delay in my response.
Regarding the illustrations, yes, using a tactile graphic for the arrows that show a movement from one value to another and also using a tactile graphic to show how many "hops" an animal makes, would most nearly capture the print's visual/spatial explanation of math concepts.
For the cross"word" puzzle, I agree with your reasoning that you should give the number of spaces that print provides for the answer.
I understood from your question that print provides a space in the crossword grid for a comma; so, "1,234" would have five spaces. If that is the case, then this should be explained in a transcriber's note (for example, "If an answer includes a comma, the number of spaces provided for that answer includes a space for the comma").
Braille on!
–Kyle