Reconstructions, transcriptions and critical editions
[Eldengtei 额尔登泰, Oyundalai 乌云达赉] (1981). [《蒙古秘史》校勘本 — source edition from which the 1984 Uyghur-Mongolian-script version was transcribed]. 内蒙古人民出版社 Öbör mongγol-un arad-un keblel-ün qoriy-a [Huhhot]; 1981年3月第一版第一次印刷 (as stated in the note)
Shiratori K. (1942). Onyaku Mobun gencho hishi. Toyo Bunko publ.
Šongqor (Shuang Fu 雙福) (2001; repr. 2002). "Mongγol-un niγuča tobčiyan"-u sergügelte (Original Manuscript and Studies of "the History of the Mongols"). Hohhot
Street J.C. (1997). The Secret History of the Mongols, text in transcription, draft of 24 March 1997 (diskette)
The Historical Corpus of the Mongolian Language (mongoliancorpus.org) contains the full text of the Secret History in I. de Rachewiltz's transcription, split into sentences, with an English translation and morphological annotation. You can search for a word form, lemma or grammatical category and get every example from the text alongside examples from other Middle Mongolian sources.