If your concerns are mitochondrial DNA, you can get that from most cells, meaning that it would be easy for Mal's dad to get access to it, though, I don't really see the point (as the material it codes for isn't likely what he wanted to duplicate). I do agree with your statements about epigenetic factors influencing the child, so she's less likely to match the original than an identical twin would be.
As to whether she is related to the MC, that varies from place to place, but it's extremely likely that a clone would be "related" to the family of the original. In the USA, 
	
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 specifically mentions that human cloning should be prevented because of its effect on "kinship relations" for the parents and child, implying that the familial relation is there in order to be affected. Furthermore, HR 3498 repeatedly refers to the cloned person as a child of the genetic donor(s), so this would almost certainly fall under brother-sister incest regulations (which vary by state) if they return to the USA.