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You seem to be asking for a definitive verse in scripture that states or implies that the soul has a gender. There is no such verse (it seems), and indexes to mentions of gender list nothing concrete. However:
God made humans, "in the image of God he created them; male and female he created them" (Genesis 1:26), and this was so before the fall. This passage is used to show that human persons are male or female.
The body will rise, for "It is sown a natural body; it is raised a spiritual body". This passage is used to show that the perfection of a person includes both soul and glorified body. A person is not soul, not body, but the unity of both.
A soul is a male soul in the sense of being the soul of a male person: a person with a male nature. Your hand has no gender, your blood has no gender. In that sense a soul has no gender.
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Using the King James translation, the soul is female:
My soul shall make her boast in the Lord: the humble shall hear thereof, and be glad. (Psalm 34:2, KJV)
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Is there a biblical basis that suggests gender is not merely biological/physical?
I would say that the principal argument in favor of the assertion that gender is not limited to physical creatures, is that God the Father is spirit (John 4:24) and invisible (1 Tim. 1:17), yet He is always referred to by masculine-gendered pronouns in the New Testament. One would think that, if gender was only a trait possessed by physical creatures, God would simply be referred to by neuter-pronouns (e.g., αὐτό ("it")). In addition, He is frequently referred to as "father" (and then, never "mother").
God is called "father" and referred to by the male gender for several reasons, including:
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The Catechism of the Catholic Church #239 specifically states that "God is neither man nor woman: he is God":
239 By calling God "Father", the language of faith indicates two main things: that God is the first origin of everything and transcendent authority; and that he is at the same time goodness and loving care for all his children. God's parental tenderness can also be expressed by the image of motherhood,62 which emphasizes God's immanence, the intimacy between Creator and creature. The language of faith thus draws on the human experience of parents, who are in a way the first representatives of God for man. But this experience also tells us that human parents are fallible and can disfigure the face of fatherhood and motherhood. We ought therefore to recall that God transcends the human distinction between the sexes. He is neither man nor woman: he is God. He also transcends human fatherhood and motherhood, although he is their origin and standard:63 no one is father as God is Father.
To make it simple, what I take away from the "whole picture", is that there is NO difference in the spirit and soul. Made in the image of God, the alpha and the omega, our bodies just express the spirit in different ways, almost to the point that gender is just as analogous to type A vs. type B personality.
In conclusion, we have male and female bodies made from the dust of the earth, with God (no sex) inside.