score:4
Basically, as far as travel is concerned, she'll have to convince the border officer, each time she tries to enter, that she's not trying to live in the US. Each time she's admitted, she'll be allowed to stay for six months, unless the officer explicitly admits her for a shorter period.
The substantial presence test is for determining whether a foreign national is a resident of the US for income tax purposes. It has no bearing on immigration status.
The risk you should be concerned about is a border officer refusing entry because she appears to be living in the US. I suppose that this will be more likely after she finishes her studies.