Is my marriage to my wife valid, and must I renew the marriage contract, and what must I do, given that her father was not present at the first marriage contract?

You have done well by repenting to Allah, and you must be careful in the future not to be lenient in dealing with women by being in seclusion. Your marriage to the woman after her divorce has two possibilities:

1. Her husband did not consummate the marriage with her: She has no waiting period ('iddah). The issue of the guardian (wali) remains, as marriage is valid without him according to Abu Hanifa, and it is permissible to adopt his view here, especially given the long passage of time and the birth of children.

2. Her husband consummated the marriage with her: You married her while she was in her waiting period ('iddah), and the marriage of a woman in her 'iddah is invalid by consensus. The children are attributed to you if you believed the marriage was valid. For any marriage where the husband believed it to be permissible and engaged in sexual intercourse, the child is attributed to him, and they inherit from each other by agreement of the Muslims, even if the marriage was invalid in itself.