Thank you for the question and sorry for the delayed response. Yes, you are correct -- please transcribe the abbreviated words exactly as you see them. You should not add any missing letters, but if you do come across an abbreviated word that you think would be significant to a researcher, you can always add a tag that includes the fully un-abbreviated word.
If you have an example that you would like to share, please pass it along and I will consult further with one of our Latin specialists.
As for the punctuation, I have noticed this quirk as well, and would encourage you to take essentially the same approach as mentioned above -- just transcribe the text as it appears, even when the spacing and placement of punctuation might seem strange.