Shalom and Hag Sameach!
1) If it’s prohibited for a woman/girl to wear a pajamas (garment for men?)
2) If it’s permitted to separate challa from baked goods (3 different types) in the case when 16 cups of flour was used for
all of them, but someone ate from them already before separating challa?
Pajamas are generally “unisex,” meaning meant for men and also for women, and it is the ordinary way for women to wear them, so that there will not be a prohibition. If the pajamas are clearly menswear, and women would not generally wear them, they should not be worn. Please see here for a previous post on a similar question.
It is permitted to take challah from baked goods, even after somebody has eaten from them. The baked goods would have to be joined together, by placing them into one basket, or under one cover. Note that the baked goods only join together if they are all of the same type of goods, so that one wouldn’t mind their actual joining together.