Qur'an Compilation

What were the differences, if any, between the Quran compiled by Imam Ali and Uthman? If there were differences how do we know what we have today is unaltered? Amina Inloes	Why were the abrogated orders not removed before the final Quran was compiled? How can a reader of the Quran avoid getting confused by a verse that talks about such an abrogated command? Sayyed Mohammad Al-Musawi
Is the Quran gathered and compiled by the first three caliphs or by the Prophet Muhammad SAW himself? Sayyed Mohammad Al-Musawi	Were the 114 chapters of the Qur'an written in chronological order? And if not, why were they not compiled in such a manner? Sayyed Mohammad Al-Musawi