The following mods need to be below Project Valkyrie and Outcasts & Remnants in your load order

Satellite World Map by Floor Below (to prevent issues with map icons not showing up in the right places)

If you're running a mod that overhauls the interior of the Prydwen or Institute, put that mod BELOW OutcastsAndRemnants.esp and ProjectValkyrie.esp in your load order. 

OAR and PV don't move any vanilla assets in those cells, they only add a few invisible objects like idle markers.  However, any Prydwen/Institute mod that moves things like vanilla walls, plane markers, room markers, etc, could cause visual glitches unless that mod is lower in load order.

Examples include Elianora's Faction Housing Overhaul, Enhanced Prydwen Overhaul, Enhanced Prydwen Overhaul 2.0, Institute Rebuilt Prydwen Overhaul, A Sensible Prydwen Overhaul, Prydwen Player Home, David Hunter, Hilda Hughes.

These all need to got BELOW OutcastsAndRemnants.esp and ProjectValkyrie.esp in your load order.

With respect to Hilda Hughes - An Institute Story, the additional rooms and NPC's it adds will no longer be present if you choose to reform the Institute in "The Revolution will not be Televised" quest. If you have that mod installed, complete its story first before you complete "The Revolution will not be Televised".  You'll get a reminder warning in-game if you're about to make a choice that cuts off certain Institute-related content.

Green grenade arc missing in certain interiors

When throwing grenades in Fallout 4, a green arc shows up that helps you aim if you have the 2nd level of the demolition expert perk.  In certain interiors, for certain users, this green arc doesn't show up.

The green grenade arc still shows up outdoors.  It just doesn't consistently show up in all interiors of this mod, but the grenades still work as normal in those areas except for the green arc.

Power armor can become invisible when you abandon it in interiors with low ceilings

When you exit power armor in the B.O.G bunker in an area with a low ceiling, remember where you left it. This issue is due to room markers. A room marker is used for optimization, so that objects in other rooms aren't loading while you're not looking at them. But when a room marker is in between a ceiling and a floor, and the top of the power armor is up near the ceiling, it can make the power armor invisible when you exit it. This is unfortunately a vanilla "feature" associated with power armor and room markers, so we can't do much about it.

Owen Stimpak animation and power armor

Owen uses a custom race, just a variant of the child race that allows combat. You can Stimpak him like normal, but the Stimpak animation won't play.

Don't put Owen in power armor.  Not meant for kids.  If he gets in Power Armor, you can ask him to exit.

Forest Grove Marsh battle

If you have a landscape mod installed that affects precombine/previs (e.g. a combo of Regrowth Overhaul with Beantown Interiors), some of the buildings on the west end of town may flicker during the BoS/ghoul battle.  It's not an issue with Project Valkyrie. If you're getting flickering, stick to the east end of Forest Grove Marsh, which is a tactically superior position for the battle anyway.

Atlas Summit and Glowing Sea Detention Center

There is an Easter Egg called the Glowing Sea Detention Center.  It's in the Glowing Sea, south of Virgil's cave, and it's the place where anyone you banished from the Institute (with the teleportation gun) ends up. No quests run to this location, and it's optional to visit.

There is a mod called Atlas Summit which makes extensive landscape alternations to the area and buries the Glowing Sea Detention Center under the ground. If you run Atlas Summit, and still want to access the Glowing Sea Detention Center, use the following console command to get in: coc aaSinstitutePrison. Or use a TCL console command to walk through the obstruction from Atlas Summit.

Quest marker when turning in Reformed Institute quests

When out in the Commonwealth doing a quest for the reformed Institute, when it's time to turn in the quest, sometimes the quest marker will be pointed at Club Snuggle (which has a teleport pad to the reformed Institute) rather than at the Institute.  You can follow the quest marker, but it's quicker to just fast travel directly to the Institute.