A majority of the latter day Shia deny the belief of interpolation in the Qur’an which is attributed to them. They claim that their scholars, by consensus, are of the view that the Qur’an is protected from change.
We say this as Taqiyyah which becomes quite evident by referencing their relied upon sources. We shall present the reality of this and in light of which we will understand the view of Khomeini.
ان الاخبار قد جاءت مستفيضة عن أئمة الهدى من آل محمد صلى الله عليه وسلم باختلاف القرآن وما أحدثه بعض الظالمين فيه من الخلاف والنقصان
The narrations of the guided Imams from the descendants of Muhammad salla Llahu ‘alayhi wa sallam regarding the differences in the Qur’an and the interpolations brought about by the oppressors are many and widespread.
Now, to determine the true stance of Khomeini we shall revert to his own words and methodology, not employing conjecture or mere opinion.
Firstly, he draws and takes cues from many books, the authors of which ascribe to the belief of interpolation of the Qur’an. For example:
i. The book, Mustadrak al Wasa’il. He also sends prayers of mercy for the author. The same author has also written Fasl al Khitab.
iii. The book al Wasa’il of al Hurr al ‘Amili who is of the same belief.
iv. The book, al Ihtijaj of Ahmed al Tabarsi. The author holds extremist fringe beliefs regarding the Qur’an. Yet we find all the Shia and above all Khomeini revering this man, drawing from him, and acknowledging his virtue. This despite his errant beliefs.
Secondly, Khomeini states in his work Tahrir al Wasilah:
یکره تعطيل المسجد ، وقد ورد أنه أحد الثلاثة الذين يشكون إلى الله عز وجل
It is disliked to abandon a Masjid. It has been related that it (the masjid) is one of the three that will complain to Allah subhanahu wa ta ‘ala. 
Referencing one of the relied upon works of the Shia, al Khisal of Ibn Babuwayh, whom they refer to as al Saduq (the truthful), we find the following narration to have been related in two different wordings. One of the accounts is as follows:
يجيء يوم القيامة ثلاثة يشكون إلى الله عز وجل : المصحف والمسجد والعترة .. يقول المصحف یا رب حرقوني ومزقوني
This narration indicates to the Shia belief regarding the Qur’an.
Khomeini has incorporated another text which states:
ومصحف معلق قد وقع عليه غبار لا يقرأ فيه
And a mushaf, hanging and dusty, not being recited.
This is in reference to the complete and hidden mushaf that lies with their Imam. They deem this mushaf to have been abandoned by the ummah due to the rejection of it by Abu Bakr radiya Llahu ‘anhu and those with him when it was presented to them by ‘Ali radiya Llahu ‘anhu—a fable of their fables.
Thirdly, we have before us an important document that denounces the claims of these Ayatollahs regarding this Qur’anic issue and exposes their Taqiyyah. The document we talk of is an Urdu book that has been endorsed by several of their contemporary Ayatollahs; amongst them Khomeini. The names of endorsement appear in the beginning of the book in the following manner:
This book also has within it Arabic texts that outline the manner of cursing the two idols of the Quraysh, who according to them are, Abu Bakr and ‘Umar radiya Llahu ‘anhuma. It also accuses them of interpolating the Qur’an. Hereunder is a reproduction of the text form the book:
بسم الله الرحمن الرحيم اللهم العن صنمي قريش وجبتيها وطاغوتيهما وافكيها وابنتيهما اللذين خالفا أمرك وأنكرا وحيك وعصيا رسولك وقلبا دينك وحرفا كتابك
In the name of Allah, the Kind, the Merciful. O Allah send Your curses upon the two evil, lying idols of the Quraysh and their daughters who disobeyed Your command, rejected Your Revelation, defied Your Prophet, changed Your religion, and interpolated Your Book.
 Awa’il al Maqalat, pg. 98. Al Matba’ah al Haydariyyah, Najf. The foreword to this book has been written by a contemporary scholar of theirs whom they call Sheikh al Islam al Zanjaji.
 See the foreword to Tafsir al Qummi, pg. 34
 Tafsir al Safi, vol. 1, 6th foreword.
 Vol. 1 pg. 152
 Al Khisal, vol. 1 pgs. 174-175.
 Ibid, vol. 1 pg. 142.
 Tuhfah al ‘Awam Maqbul Jadid, pg. 422.