Firstly: 

It is not possible for a Muslim to entertain doubts concerning the immutability of the Qur’aan, because Allaah has guaranteed to preserve the Qur’aan. Allaah says (interpretation of the meaning): 

“Verily, We, it is We Who have sent down the Dhikr (i.e. the Qur’aan) and surely, We will guard it (from corruption)”

[al-Hijr 15:9]

The Qur’aan was preserved in the hearts of the Sahaabah who had memorized it, and on the trunks of trees and thin white stones until the time of the caliph Abu Bakr al-Siddeeq (may Allaah be pleased with him). During the Riddah wars many of the Sahaabah who had memorized the Qur’aan were killed, so Abu Bakr (may Allaah be pleased with him) was afraid that the Qur’aan may be lost. He consulted the senior Sahaabah concerning the idea of compiling the entire Qur’aan in one book so that it would be preserved and would not be lost, and this task was entrusted to the great hafiz Zayd ibn Thaabit and others who had written down the Revelation. Al-Bukhaari narrated in his Saheeh that Zayd ibn Thaabit (may Allaah be pleased with him) said:  

“Abu Bakr As-Siddeeq sent for me when the people of Yamamah had been killed (i.e., a number of the Prophet's Companions who fought against Musaylimah). (I went to him) and found 'Umar bin al-Khattaab sitting with him. Abu Bakr (may Allaah be pleased with him) said (to me), ‘ ‘Umar has come to me and said: “Casualties were heavy among the Qurra' of the Qur'aan (i.e. those who knew the Qur’aan by heart) at the Battle of Yamaamah, and I am afraid that more heavy casualties may take place among the Qurra' on other battlefields, whereby a large part of the Qur'an may be lost. Therefore I suggest that you [Abu Bakr] should issue orders that the Qur’aan be collected.” I said to 'Umar, “How can you do something that the Messenger of Allaah (peace and blessings of Allaah be upon him) did not do?" 'Umar said, “By Allah, this is something good.” ‘Umar kept on urging me (to accept his proposal) until Allah opened my heart to it and I began to realize the good in the idea which 'Umar had realized.’ Then Abu Bakr said (to me): ‘You are a wise young man and we have a great deal of confidence in you. You used to write down the Revelation for the Messenger of Allaah (peace and blessings of Allaah be upon him). So you should seek out the Qur’aan [i.e., the fragments on which it is written] and collect it (in one book).’ By Allaah, if they had ordered me to move one of the mountains, it would not have been harder for me than this command to collect the Qur’aan. I said (to Abu Bakr), ‘How can you do something which the Messenger of Allaah (peace and blessings of Allaah be upon him) did not do?’ Abu Bakr said, ‘By Allaah, it is a good thing.’ Abu Bakr kept on urging me (to accept his proposal) until Allah opened my heart to it as He had opened the hearts of Abu Bakr and ‘Umar. So I started to look for the Qur’aan and collected it from (the fragments on which it was written of) palm-stalks, thin white stones and the hearts of men (i.e., from men who knew it by heart), until I found the last verse of Soorat al-Tawbah with Abu Khuzaymah al-Ansaari, and I did not find it with anybody other than him. The verse is :  

‘Verily, there has come unto you a Messenger from amongst yourselves. It grieves him that you should receive any injury or difficulty…’

[al-Tawbah 9:128 – interpretation of the meaning]

… until the end of Soorat Baraa’ah (Soorat al-Tawbah). 

These fragments remained with Abu Bakr until he died, then with ‘Umar for the rest of his life, then with Hafsah bint ‘Umar (may Allaah be pleased with them both).” 

Secondly: 

With regard to al-Hajjaaj, it was not his idea to write out the Mus-haf, rather he was commanded by an intelligent man to do that. There follows the complete story: 

Al-Zarqaani said: 

It is known that the Mus-haf of ‘Uthmaan was unpointed (i.e., it had no diacritical marks). Whatever the case the addition of diacritical marks to the Mus-haf did not happen, according to the well-established view, until the era of ‘Abd al-Malik ibn Marwaan, when he realized that Islam had spread widely and the Arabs were mixing with the non-Arabs, which was having an effect on the Arabic language, so that there was much confusion about the correct reading of the Mus-hafs and it was becoming very difficult for people to tell the letters apart. By his deep insight, he realized that he should do something to solve the problem. So he commanded al-Hajjaaj to take care of this important matter. In obedience to the caliph, Al-Hajjaaj appointed two men to deal with this matter, namely Nasr ibn ‘Aasim al-Laythi and Yahya ibn Ya’mar al-‘Adwaani, both of whom were qualified and able to do the task required of them, because they were knowledgeable, righteous, pious and experts in Arabic language and the various readings of the Qur’aan. They had also both studied under Abu’l-Aswad al-Du’li. May Allaah have mercy on these two shaykhs, for they succeeded in their work and gave the Mus-haf diacritical points for the first time. They added dots to all the letters that look similar, not adding more than three dots to any one letter. That became widespread among the people and was very effective in dispelling confusion concerning reading of the Mus-haf.  

It was said that the first person to add diacritical marks to the Mus-haf was Abu’l-Aswad al-Du’li, and that Ibn Seereen had a Mus-haf to which diacritical marks had been added by Yahya ibn Ya’mar. These opinions may be reconciled by noting that Abu’l-Aswad was the first one who added diacritical marks to the Mus-haf, but he did that for his own individual use, then Ibn Seereen followed him in that, and that ‘Abd al-Malik was the first one to add diacritical marks to the Mus-haf  in an official and public manner that was spread widely among the people in order to dispel any confusion with regard to reading Qur’aan.” 

Manaahil al-‘Irfaan, 1/280, 281 

Thirdly: 

With regard to what is mentioned in the question, quoting from al-Masaahif by Ibn Abi Dawood, there follows the report concerning that and the ruling thereon: 

It was narrated from ‘Abbaad ibn Suhayb from ‘Awf ibn Abi Jameelah that al-Hajjaaj ibn Yoosuf changed eleven letters in the Mus-haf. He said that in Soorat al-Baqarah 2:259 it said lam yatasanna wa’nzur, with no ha’, and he changed it to lam yatasannah wa’nzur (they show no change, and look…) 

In al-Maa'idah 5:48 it said sharee’atan wa minhaajan, and he changed it to shir’atan wa minhaajan (a law and a clear way) 

In Yoonus 10:22 it said, Huwa alladhi yunshirukum and he changed it to Huwa alladhi yusayyirukum (He it is Who enables you to travel…) 

In Yoosuf 12:45 it said Ana aateekum bi ta’weelihi and he changed it to Ana unabbi’ukum bi ta’weelihi (I will tell you its interpretation) 

In al-Zukhruf 43:32 it said, Nahnu qasamnaa baynahum ma’aayishahum and he changed it to Nahnu qasamnaa baynahum ma’eeshatahum (It is We Who portion out between them their livelihood) 

In al-Takweer 81:24 it said Wa ma huwa ‘ala’l-ghaybi bi zaneen and he changed it to Wa ma huwa ‘ala’l-ghaybi bi daneen (and he withholds not a knowledge of the unseen) 

Kitaab al-Masaahif by al-Sajistaani, p. 49. 

This report is da’eef jiddan (very weak) or mawdoo’ (fabricated), because its isnaad includes ‘Abbaad ibn Suhayb, whose hadeeth is to be rejected. 

‘Ali ibn al-Madeeni said: his hadeeth is no good. Al-Bukhaari, al-Nasaa’i and others said: he is matrook (to be rejected). Ibn Hibbaan said: he was a Qadari who promoted his innovated ideas, and he narrated things which a beginner in this field would realize were fabricated if he heard them. Al-Dhahabi said: he is one of those who are to be rejected. 

See Meezaan al-I’tidaal, by al-Dhahabi, 4/28. 

The text of the report is also false, because it dos not make sense that these changes could be made in the Qur’aan and then spread throughout the world. Even some of the non-Muslims, such as the Raafidis (Shi’ah) who think that the Qur’aan is incomplete, rejected this and criticized its text. 

Al-Kho’i, who is one of the Raafidis, said: “This claim is like the hallucination of one who is suffering a fever, or like the fairy tales of the insane or of children. Al-Hajjaaj was one of the governors of the Umayyads, and he is too incapable to do anything to the Qur’aan. He is even incapable of changing any of the minor issues of Islam, so how could he change the thing which is the foundation of the religion and the basis of sharee’ah? Where would he get the power to introduce this change throughout the realm of Islam and beyond at the time when the Qur’aan was well known throughout the Muslim world? How come no historian has ever mentioned this disastrous event even though it is so serious and they would have a lot of motives to mention it? How come no one among the Muslims of his time narrated it? How could the Muslims have turned a blind eye to such an action after the reign of al-Hajjaaj came to an end? Even if we assume that he could have gathered all the copies of the Qur’aan and that not one single copy escaped his grasp anywhere in the far-flung regions of the Islamic world, how could he have removed it from the hearts of the Muslims and those who had memorized it, the number of whom at that time is known only to Allaah.” 

(al-Bayaan fi Tafseer al-Qur’aan, p. 219) 

What the questioner mentions about Imam al-Sajistaani, and that he wrote a book called Ma Ghayyarahu al-Hajjaaj fi Mus-haf ‘Uthmaan (What al-Hajjaaj altered in the Mus-haf of ‘Uthmaan) is not true, rather it is a blatant lie. All there is, is the commentary that al-Sajistaani wrote concerning the words quoted above from al-Hajjaaj, entitled Baab Ma Kataba al-Hajjaaj ibn Yoosuf fi’l-Mus-haf (Chapter on what al-Hajjaaj wrote in the Mus-haf). 

On this basis, we cannot rely upon this report under any circumstances whatsoever. The fact that until now it has not been proven that anyone has succeeded in his attempt to change even one letter (of the Qur’aan) is sufficient to prove that it is a lie. If what has been narrated is true, then it would be possible to repeat it, especially at the times when the Muslims were weak and their enemies plotted against them.  It is such specious arguments that prove that these claims are false, and that our enemies are incapable of refuting the evidence of the Qur’aan or its clarity, so they resorted to attacking it. 

And Allaah knows best.