What is the ruling on one who denies a letter or a word from the Book of Allah, and do the rulings of disbelief apply to recitations such as Warsh and Qalun, which may seem different from the continuously transmitted Hafs recitation?

I appreciate your zealousness for the Quran, but you were too quick to deny what you did not fully understand. These very letters are as they are in the Uthmanic Mus'haf. As for the differences found among the seven reciters, where some add letters and others omit them, it is because Uthman wrote these instances in some copies and not in others. This was to indicate that all of it is valid and that recitation with any of them is permissible.

The Basmala, in some recitations like that of Ibn Kathir, is a verse of the Quran, while in others it is not. There is nothing strange in this. The word "huwa" (هو) in His (Allah's) saying, "فَإِنَّ اللَّهَ هُوَ الْغَنِيُّ الْحَمِيدُ" (Indeed, Allah - He is the Free of need, the Praiseworthy), is a word from the Quran in the recitations of Ibn Kathir, Abu Amr, Asim, Hamza, and Al-Kisa'i, but it is not from the Quran in the recitations of Nafi' and Ibn Amir, who recited, "فَإِنَّ اللَّهَ الْغَنِيُّ الْحَمِيدُ" (Indeed, Allah is the Free of need, the Praiseworthy). The waw (و) in His (Allah's) saying, "وَقَالُوا اتَّخَذَ اللَّهُ وَلَدًا" (And they said, "Allah has taken a son"), is from the Quran according to the recitation of the seven reciters other than Ibn Amir, while in Ibn Amir's recitation, it is not from the Quran, for he recited, "قَالُوا اتَّخَذَ اللَّهُ وَلَدًا" (They said, "Allah has taken a son") without a waw, and it is omitted in the Mus'haf of the people of Sham.

Know that the Ummah has unanimously agreed that one who affirms the Basmala or one who negates it does not disbelieve, due to the difference among scholars concerning it. This is unlike denying a letter upon which there is consensus, or affirming what no one has said, for in those cases, one disbelieves by consensus. There is no disagreement that it is a verse within Surah An-Naml, and there is no disagreement regarding its written affirmation at the beginning of the surahs in the Mus'haf, except at the beginning of Surah At-Tawbah. We advise you to read what scholars have written on this subject before rushing to deny.