Below is a collection of troubleshooting topics.  Installation issues are listed first.  Play-through issues are listed second.  Check the Quest Details article in the articles section if you get stuck on a particular quest and need a workaround.

If you run across a bug, any detail you can provide in the bug reports section (not the general comments section) is appreciated.

Installation Issues

When I install, the mod manager asks if I want to overwrite the files from another mod.  What should I do?

This mod uses assets, with permission, from various other mods.  When installing you might receive a message about whether you want to overwrite existing files from the following mods:

Deadric Reaper - DX Mini Armor Collection by Deserter X and Mitosuke
Tembtra Thief Outfit by Deserter X and Mitosuke
Emfy Cleric Armor by Deserter X and Mitosuke
Legendary Armors - DeserterX Collection (which uses the 3 outfits above)

Shouldn't matter how you answer, they are the same texture/mesh files, but easiest path is "yes to mod" or "no to mod". 

This mod also edits face meshes and texture files for Elisif.  If you receive an overwrite message for one of the following files:

Mesh file: FaceGenData > FaceGeom > Skyrim.esm > 0001326A.NIF
Texture file 1: FaceGenData > FaceTint > Skyrim.esm > 0001326A.dds
Texture file 2: FaceGenData > FaceTint > Skyrim.esm > 0001326A.tga

Answer "yes to mod".  You need to use the Elisif face meshes and textures from this mod to avoid the dark-head bug. 

Examples of other mods that edit Elisif's NPC record are Aesthetic Elisif, QD Characters, Nexus Skyrim Overhaul SSE, Toccata Follower (if Elisif Replacer option is chosen), and Follower Cynthia the Spell Lady and Elisif Replacer SE. More detail here.

Nexus Mod Manager (NMM) is having a problem installing the file.

Check the Nexus Forums (or Google). NMM installation errors can occur with larger files, if you're not running it in admin mode, or if your anti-virus program conflicts with it.

To avoid audio problems, do not install using the Download NMM button on the main mod page.  Download Manual, and then dragging the file into your mod manager, is the most trouble-free way of doing it.

Play-through Issues

I lost Aurelia, Jesse, Sam, or Elisif.  How do I find them?

Check your conjuration spells under the Magic menu.  Each companion comes with a teleport spell you can use to teleport them back to you if they get lost.

Aurelia, Jesse, Sam, or Elisif aren't giving me new quests.

Ask them about something else, exit the conversation, then talk to them again.  If that doesn't work, travel with them to a new location in a different hold.  Some of the quests are coded as "change location events" so you have to change location for a new quest to trigger.

There isn't a quest marker or one of the quests is bugged.

Sometimes the repeatable quests will send you to locations in Solstheim (Dragonborn), in which case you have to travel to Solstheim before the map marker shows up.

See the Quest Details article if you get stuck on one of the main quests.  If it's a repeatable quest (bounties, word of power, skill book, enchanted gear, drug dealer, war loot, explore new places, Dwemer ruin, Dragon Priest lair), just ask the companion who gave you the quest to stop it.  Travel somewhere else and they'll give you a new one.

The Lost Knife Cage Key doesn't open the cage with the prisoner in Coldwater Cave

The Lost Knife cage key opens a cage in Lost Knife Hideout. It doesn't open the cage in Coldwater Cave. Follow the quest markers to open the cage in Coldwater Cave.

I accidentally attacked a companion and now they are attacking me back.

Move to a new cell, get in a fight with some enemy NPC's, or reload your latest save.

NPC's aren't spawning where they should and/or the area is empty.

This is a "feature" of Bethesda games.  Use hard saves as you play through, not quick saves or exit saves. If you don't see enemies or NPC's showing up where they should, exit the game completely (to desktop, not just main menu), and re-load the game. If that doesn't work and you've used quick saves or exit saves to reload the game, start from the most recent hard save.

A quest marker is telling me to return an item I found to a companion

Return the item to the companion to complete the quest.

I only downloaded this mod so I could destroy the Zynimax Creation shop.  How do I get that quest?

First complete the quest "Disarm and Destroy" that Sam gives you.  Then ask him where he got his armor from, and he'll give you the quest "Taste for a Cure", which at one point lets you blow up the Zynimax Creation Shop.

How do I get the quest "Set the Building on Fire" to blow up the Thalmor Embassy?

Kill Alduin, finish Jesse's other quests, then ask "Are you alright, you look upset?", and he'll give you the quest.

The battles are too hard

Change your difficulty settings in game settings, or get better at not dying, or craft better armor and weapons at a crafting station.

I want to change the follower distance

Aurelia, Sam and Jesse are set to the same follower distance as each other (floats between 180 and 360), but it's easy to adjust any one of those in SSEEdit. Under packages, the package names are:

SB_SamFollowPackageStage20
SB_JesseFollowPackageStage20
SB_AureliaFollowPackageStage20

Then scroll down to the package data section, and adjust the values to whatever you want (e.g. 300 and 500 instead of 180 and 360).