Praise be to Allah, the Lord of the Worlds; and may His blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions.
Your question consists of many matters.
First, the matter of the negligence of the prayers of your wife, if she believes that they are obligatory, Muslim scholars have different opinion concerning the person who neglects the prayers without denying their obligation. The majority of Muslim scholars are of the opinion that she commits a minor Kufr that does not take her away from Islam, but she is in a great danger.
Some others are of the opinion that if the ruler asked her to repent from neglecting prayers and she does not make repentance then she becomes Kafir.
A third group is of the opinion that whoever neglects prayers becomes Kafir.
Second, we cannot take any decision about her hesitation in the matter of Hajj; maybe due to a defect in her faith or maybe for another reason.
Third, as for her saying ‘So far yes’ when she is asked about the finality of the Prophet (Sallallahu Alaihi wa Sallam), it indicates that she may change her faith in future, no doubt if she means that, then it is Kufr and apostasy from Islam. If she says so meaning something else then we cannot conclude her Kufr.
Fourth, as for her keeping quiet when she is asked about Qur'an whether it is the word of Allah or not, we do not know why she kept quiet whether it was due to affirmation or negation so, based on her keeping quiet we cannot issue any decree.
Finally, our advice is to try your best to explain to her the Islamic faith in a good and pleasant manner.
However, if it is proved without any doubt that she does not believe in Angels, in Qur'an and that she may change her faith regarding the Prophet (Sallallahu Alaihi wa Sallam) Muhammad then it is apostasy from Islam and the marriage with her will be cancelled from that time.
If she repents from that during her Iddah you may take her back without any new contract according to the preponderant opinion of Muslim scholars.
If she repents after her Iddah is completed then if you want to take her back, you have to renew the marriage contract fulfilling all the conditions of a valid marriage.
Also, we advise you to provide her with Islamic books, cassettes, articles that address her doubts. It is better to arrange meetings with the scholars who can remove her doubts and help her understand Islam well.
We supplicate Allah to correct your wife and guide her to the right path.
Allah knows best.