Should the sister marry the suitor whom she does not feel comfortable with after performing Istikhara, despite her initial approval of him and his good character?

The criterion for the outcome of Istikhara is the facilitation of the matter, not merely a feeling of unease. If the suitor is a man of religion and good character, the sister should agree to marry him. There is no harm in repeating the Istikhara prayer; if there is good in it, she will be guided to it, and if not, Allah will avert him from her.