No, you will not have a penalty. The 5329 is for her return since she didn't get it all taken. When the program asks about RMD, select the she did not take the full amount. This will lead you to the 5329.
I went through it with my parents so I understand where you are and how hard it is. I filled out the 5329 and had no issues. I took the RMD and put in on my return. No issues. You are doing well.
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