Ok this is the timeline I have so far that I will be using,

  In background The Imperial Truth philosophical would be developed for ter establishment.

  The initial, experimental phase of the Adeptus Astra Telepathica during the Unification Wars.

  The Creation of the Adeptus Astra Telepathica: a early small testing of how this could be done on a rge scale and what method should be used.

  The Unification Wars: The absolute starting point. The Emperor consolidates power on Terra, forging the nascent Imperium with the Thunder Warriors and Custodians.

  As well The principles of the Imperial Truth are applied but not yet codified.

  The Pacification of Luna: This logically follows the victory on Terra. Securing the moon and its vital gene-cults was the next step before the Emperor could look outward to Mars.

  After the pacification of Luna a short "development" period where he and his closest advisors (like Malcador) look at Imperial Truth's.

  The Alliance with Mars (Treaty of Olympus Mons): With Terra and Luna secured, the Emperor needed Mars's technological might. This treaty is the foundation for all future military and technological development.

  After The Alliance with Mars a short "development" period where he and his closest advisors (like Malcador) look at Imperial Truth's.

  The Primarch Project starts now: This is the Emperor's grand ambition, initiated with the Mechanicum's resources. It's the central project of this era, happening concurrently with other developments. The scattering by Chaos occurs during this phase.

  This project was a decade in the making the scattering happened helf way development.

  Begin now for full establishment of the Council of Terra (governing body during the Emperor's absences) ter.

  At this time the council was purely administrative, managing the rebuilt Terra and assisting with the bureaucracy of government.

  The Astartes Project's Early Failures and Refinement of the Astartes Process: This occurs after the Primarchs are scattered. The Emperor, robbed of his generals, turns to their gene-seed to create the Astartes. This section represents the initial, imperfect attempts before the final process was perfected.

  This was a necessary period of perfecting the gene-seed techniques after the loss of the Primarch temptes.

  Official organisation public beginning The Creation of the Adeptus Astra Telepathica: As the Emperor pns for interstelr travel, he must address the psyker problem. Organizing them is a critical step for both communication (Astropaths) and security.

  The Development of Warp Travel Technology: Working in tandem with the Astra Telepathica, the Emperor and Mechanicum refine the technology needed for a gaxy-wide crusade. This is the practical application of their alliance.

  The development of the Navigator Houses' formal alliance with the Imperium

  The Culling of the Thunder Warriors: This happens after the Astartes are successfully created and are proving to be a stable and superior repcement. The old guard is eliminated to prevent them from becoming a threat to the new order.

  The Formation of the Imperial Army: With the Astartes as the spearhead, the Emperor builds the conventional military force that will serve as the bulk of his expeditionary fleets, drawing on the veteran regiments from Terra and Luna.

  It would be the formal amalgamation of the veteran Terran and Luna regiments from the Unification Wars, now standardized with Mechanicum weaponry and organized into the Expeditionary Fleet structure

  The formation of the first Legiones Astartes (immediately before the Great Crusade begins)

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  Crusade starts.

  As the crusade starts to get going the Council of Terra's Full Role begin to show itself its powers and composition starting to expanded and formalized as things start to become big.

  This is done by Charter of the Council of Terra" issued by the Emperor just before he departs for the Great Crusade, defining its powers in his absence.

  The Sisters of Silence are found and ter refined by the emperor : You're correct that they were discovered during the Crusade, not before. This event should technically be moved to the beginning of the Great Crusade timeline, not the pre-Crusade one.

  The Imperial Truth: This is the state ideology that formally begins with the Great Crusade. It's the philosophical justification for the Crusade itself and is enforced as the Emperor's fleets expand into the gaxy.