Hi Susan. Your transcription of the four electron dot configurations is exactly correct. Isn't it nice how simple they are? It's not clear to me in your simbraille example if you have the same number of blank cells between each atom. Three blank cells is standard. No, you do not need to show the box lines around them. Yes, you should list the two bonds on a Special Symbols page. Use the heading "Electron Dots" and use the same description as you find on page 12 of the Chemistry Code.
I am guessing that the chemistry questions are scattered around the test, not all grouped together? If so, it is best to use the same code throughout the test. Including punctuation indicators with all scientific abbreviations will not hinder the reading in any way. State on a Transcriber's Notes page that all material on the test is brailled following the rules of the Braille Code For Chemical Notation 1997.
If, instead, all the chemistry questions are grouped together, you can insert a transcriber's note at that point stating that the rules of the Braille Code For Chemical Notation 1997 are used for questions # - #.
Thank you for your question.