DreamKingMods

I know it's only a small part of your post--which has lots of good ideas--but I wanted to note that there is already mod that does this.

There's a bug in the 1.6 update itself which is causing this--hopefully Bethesda will release a patch soon. The 1.6 update has a bug that causes any mod that edits the default game's dialogue to break that dialogue. Until this is fixed, it is likely not going to be possible to "fix" mods like this one (and after the Bethesda bug is fixed, this and other mods should work again without need a of a fix).

I should add to what I wrote before--you may also be able to give followers Perks via console commands. Not sure if that works. If it does, you could use the console to give your follower a perk each time you level up yourself. That works better if you only have one or two consistent followers, of course.

Have you resolved this with the Nexus staff already? The URLs to mods changed when the site code was updated, and some of the site features may have been in flux. I can see your mod now just fine. (It's a great mod, BTW: nice work!)

It's not specific to the courier's dialogue--mods that edit any vanilla dialogue are causing the quests associated with that dialogue to fail after the 1.6 update. (For example the Unofficial Skyrim Patch, which fixes many typos in dialogue, has been hit hard by this.) Bethesda have been made aware of the issue and they will hopefully be issuing a further patch sooner rather than later.

What do the mod's permissions say? (It's the little "P" icon under the mod's unique download count.)

This isn't currently possible because the script command to add perks only works on the player character, not NPCs. The only way to control what perks are on followers is to manually add perks to the actor in the Creation Kit.

You may need to use the default Skyrim launcher when you first subscribe to a Workshop mod just to make sure it is checked in the Data Files area of the default launcher. However, once you've done that, you should exit out of the launcher and start the game via the SKSE loader app. You'd only need to do that when you've added new mods. After that yes, they'll be included when you launch the game via the SKSE loader. (You may also need to do the same process when you add a new Nexus mod, by the way: Workshop mods aren't special, it's just an alternate way of downloading mods.)

There isn't a TESVedit yet, but one is in the works. (And also this.)

There are actually several: SkyRe, Skyrim Improved. And do a Nexus search for words like "race" and "racial" and you find mods like Racially Motivated Overhaul, which does seem to change speeds based on race. Also note that PISE is modular, so if you want the harder spawns but not the changes to loot, you can do that.

You want to put your voice files in the folder named Skyrim/Data/Sound/Voice/MyQuest.esp/(Voiceset of the speaking actor)/ If that directory doesn't exist then create it by hand. The CK's playback button is for playing back the line just recorded so you can determine if you want to save it. To play an already-recorded sound file in the CK, you need to double-click the file name. This will only work if there is a .wav file, I believe; the CK internally won't play .xwm or .fuz files, although they should play fine in-game.

console: set playerfollowercount to 0

Using TESVsnip is not recommended--it is known to cause mod corruption/data loss in the mod being edited, because of its inability to handle certain subrecords. More info.

To the best of my knowledge: Resources in BSAs will be loaded into the game according to the user's mod load order. Conflicts between loose files can be managed fine by Wrye Bash's installation system. The real problem comes if you try to mix mods with BSAs and those with loose files--because loose files will always override BSAs. In other words, you could have a mod with a BSA positioned lower in your load order than a mod that uses loose files, but the loose files will override the BSA. I imagine that eventually the ideal is to have Bash scan the contents of BSAs to detect conflicts in archives, but that's probably a goodly ways into the future. For now, it seems best to either unpack all BSAs into loose files before installing using Bash, or to pack all loose files into BSAs before installing using your mod management method of choice.

Using TESVsnip is not recommended--it is known to cause mod corruption/data loss in the mod being edited, because of its inability to handle certain subrecords. More info.

I'm not sure if the Script Dragon creator uses the English-language version of the game, and the beta 1.6 patch doesn't work for localized game versions. So expecting him to create an update for a beta that he can't use...

I imagine that you need Flash, or another application capable of editing Flash files, to change the dialogue colors. The SkyUI team was asking about desired changes to the dialogue interface a few months ago, and improving the legibility was one of the things mentioned.

SKSE and SD are independent. You do not need one to use the other. Both do almost always need to be updated to match whatever version of the game you are running. SKSE has an update available for the 1.6 beta patch, while SD does not yet.

Keep your eye on the Unique Taverns project.

I'd also suggest making sure her class is a spell-oriented one--that will influence how much Magicka she has.

You can use SetRace to turn them into the werewolf race when combat starts, and then back to their original race when comabt ends (both via the OnCombatStateChanged event).

Yes, lack of voiced dialogue assets among the vanilla followers is a pain. For my Aela mod I just bit the bullet and decided to use silent, unvoiced dialogue for many random comments--the upside is that it lets me have her comment on locations and events in fairly detailed, specific way. For people making their followers who want to add this sort of thing, I'd suggest creating a separate quest/quests, and/or a separate branch in the Story Manager, to maximize compatibility with other mods.

There's a mod being worked on called Unique Taverns by Meek (aka Shezrie, of Oblivion modding fame) that aims to address this. There's a work-in-progress thread at the Bethesda forum.

For what it's worth, my mod for Aela has something like this--here's a screenshot with the available options. It is implemented via a magic effect that opens the menu--in this case triggered by a lesser power, although it could also be a spell or item. SKSE will make this sort of thing easier, eventually, since it will allow detecting keypresses.

Just wanted to note that I implemented this for Aela in the mod that I released today, Enhanced Skyrim Followers: Aela the Huntress. The default is that she'll transform when you use your beast form, and back when your form wears off. You actually have to earn sufficient respect from her in order to ask her not to transform when you do. She likes being a werewolf, after all, and she's not just going to stand by and let you have all the fun.