Is her marriage invalid due to the absence of most of her paternal uncles or her father's family, and her maternal uncle acting as the guardian (wali) in the contract?

The authority to give a woman in marriage (wilayat al-tazwij) is restricted to the 'asabat (agnates) according to the majority of scholars, and the maternal uncle (khal) has no such authority. If the marriage contract was concluded in adherence to the madhhab of Abu Hanifa, or if a Sharia judge ruled it valid, then the contract is sound. Assuming it was not concluded in adherence to Abu Hanifa, it should be upheld given the passage of time, as nullifying it would lead to harm. Moreover, a فاسد (invalid) marriage is treated like a صحيح (valid) one in some rulings after consummation, such as inheritance, establishment of lineage, and حرمة المصاهرة (prohibition of marriage due to affinity).