To be honest, the constant knock out and Quentin waking up is very repetitive so I have some concepts to make the transition between days smoother even by the littlest bit. (this is to assume Patch 9 doesn't change them)
Night 1 - The shovel is now absent, Quentin peers into the museum and sees the Neighbor in there. Before he can work out a way to get in The Guest shows up and Quentin flees back to the Banner. Locking it down, after nervously heading back to his pinboard room he marks that the neighbor is in the museum. He then heads to his bed and falls asleep, realizing that it's not safe outside at Night. This transitions into the nightmare.
Night 2 - Quentin picks up the photo in the neighbor's bedroom and looks it over, instead of instantly being taken to a nightmare he peers outside and notices/hears The Guest who is stalking him. He possibly takes the photo with him (it gets taken in the cutscene, it won't take place as a inventory item) as the players leaves the museum and avoids the guest on the way back to the banner. After getting back to the Banner and closing it up he puts up the photo of Aaron and Mr. Peterson (or doesn't if he didn't take it with him). Marking his progress he heads back to bed which triggers the nightmare sequence of taking the photo, this could lead to the nightmare even being playable for a short bit as you get the camera.
Night 3 - Taking his camera back, instead of taking a photo of himself (like why would he do that?) he immediately rushes back to the banner to add it back to the tool shelf, when re-entering the main lobby of the museum Quentin will take notice of the Crow chandler that's hanging and the fact that it seems to be getting loose, while seeming to be a random thing to point out, this will explain him having the nightmare. After noticing this, Quentin will have to make it back to the banner while avoiding the Guest so he can put back his equipment and get some well needed rest...right into another nightmare.
Free Roam will not be changed as its' currently a place holder. if you guys have your own ideas please put it in the comments. 