Scan The Keepers
Chorban now appears at the base of the Citadel tower, scanning the Keeper next to Avina (Previously he appeared in the middle of the Council Chambers)
The Keeper Chorban was scanning in the tower in vanilla has been moved to the side area (with the benches/mini waterfall) opposite to where Kahoku is

The Fan
Conrad Location 1: Upper Markets (Same as Vanilla)
Conrad Location 2: Courtyard outside Chora's Den
Conrad Location 3: Wards Alleyway

Negotiator's Fix
Elias Keeler will now appear after 2 main planets have been completed, and is located by the stairs leading to the human embassy. (Previously he appeared in the hallway to Flux)

Our Own Worst Enemy
Charles Saracino & Terra Firma: They will also appear after 2 main planets have been completed, and are located at the entrance to the embassy. (Previously they appeared in the Wards plaza)

The Fourth Estate
Khalisah will now only appear after Noveria has been completed. She will then ask you about your activities on Noveria, as well as a new follow-up question about humanity in the galactic community.

Planting a Bug
Emily Wong can now be found by the C-Sec elevator in the Presidium for her second encounter (Previously she appeared in the Council Chambers). Her first encounter in the Wards remains unchanged.

Missing Marines
Kahoku will now only ask Shepard to find his marines once Shepard finds out about Banes. You can find out about Banes by completing Dr Michel's blackmail quest and then speaking to Anderson about him.
The Sparta system will also now be locked until Kahoku gives you the quest.

Espionage
Mallene Calis has been moved to the upper level of the Mezzanine, near the stairway, so that she is out of Rafael Vargas' line of sight.

Ilos Generator Puzzle
Hint: Toggling a glyph will flip the state of the glyph(s) next to it.
Full solution below: