I've seen on MN while ago some teacher recommended using different coloured gen pen for each sentence. I think it was to encourage use of full stop and capital letters. But maybe you can use this method for full stop and comma as well? Before starting a new sentence in a different colour, she can look back the sentence she has written and use appropriate comma, full stop, etc.
This is an amusing demonstration of "Phonetic Punctuation" by Victor Borge, where each item of punctuation is represented by a sound. Rather OTT, but it may just encourage DD to THINK about punctuation when she is writing:
(There are various versions of it on YouTube, some in his stage show, if she wants to look for them.)
Does she understand all the main rules of punctuation?? Can she realise why it is needed in a story??
Another way might be for her to DICTATE what she wants to write, into a tape recorder, or a phone that records. She could then play it back, correcting it if necessary, and write it out when she is happy with it. She could cut out large punctuation signs, in various colours and place them in the appropriate places in the text.
There are various books on punctuation, by Lynne Truss, and David Crystal: