I was wondering if a Cohen can marry a Challalah (daughter of a Cohen who married a divorcee). I ask this in reference to an opinion in Kiddushin 66b (or around there) that says that the Mikvah is Metaher girls born from such a union.

A Cohen may not marry a Chalalah, that is a daughter of a union between a Cohen and a woman prohibited to him (e.g. a divocee). The Gemarah you referred to (kiddushin 77a) a marriage of a Chalalah to a kosher non Cohen purifies her family, so her daughter can marry a Cohen. (the daughter of a Chalal, a male born from the above union, may not marry a Cohen).