I'll let you play all mods related to your project in a minute (well, make that 5 minutes), but I'd like to reply to some things you said first. Please bear in mind that everything I may suggest is just that: a suggestion. It's your mod, so feel free to use, change, or discard anything I say.
Thanks for the detailed message. It really got me to thinking on what it is I hope to do with Pax Telvanni.
And that's a good thing. Don't open the Construction Set right now. Play the game a bit, get a feel for what's missing for you, and let Pax Telvanni slowly grow on you. When you think that you have worked out a part of it, sit down and write it down in a couple of notes. Or just open the Construction Set, and outline the quest in the dialogue window, Journal section. If you can't precisely outline the quest step for step, you haven't thought about it enough. In that case, ponder a bit more on it. You'll need a clear and detailed idea of what you're going to do in a quest, or you'll get stuck halfway through writing it.
By the way, that's how I made RoHT's quests: I had an idea what I wanted to see, took a couple of notes (only a single word sometimes), and when I thought I knew where I wanted to go, I wrote the quest's Journal entries (mostly catchwords at the beginning). Back then, I didn't know Klinn's Advice To New Morrowind Modders, but in retrospect, I headed most of his advice. Especially Patrograd's hints for creating quests are really useful.
While I'm at it, I'd also like to recommend the two tutorials you are likely to use/need the most: Skrikandi's dialogue tutorial and Morrowind Scripting for Dummies. I still use them.
Back to Pax Telvanni:
The first priority of the mod for me is to make RoHT, BuUL, LGNPC, and maybe Uvirith's Legacy to all work together as smoothly as possible.
Well... actually they do work together quite smoothly. In Uvirith's Legacy's (UL) latest version, Stuporstar even changed a quest to make UL completely compatible with RoHT, and I checked UL's latest RoHT patch. The same applies to LGNPC. For the latest instalment of LGNPC Tel Uvirith, Cyrano applied a couple of compatibility changes. BuUL is completely off my radar, though. I have never used it, and I'm not going to. I'm too happy with what mods I'm using in and around Tel Uvirith.
So, seeing that those mods already work together pretty well, I'd rather use Pax Telvanni to add new content that takes over where RoHT, UL, and LGNPC end. Well, you'll develop your own ideas while playing our mods.
On the faction quests:
I haven't thought about each and every faction yet, so I can only provide you with a couple of ideas. Please note that everything I'll say about Morrowind's quests comes from memory, so I might be wrong on a couple of details. Before you build on an idea, you'll need to make sure that its foundation is actually intact.
AshlandersI wouldn't concentrate on the Nerevarine title too much. Just about 10 days ago, I got a bug report on PES from somebody who had completed RoHT yet hadn't played the main quest far enough to be named Hortator. There are actually players who don't concentrate on the main quest at all.
Even if you require the player being Nerevarine, I can think of other, more subtle ways to persuade the Ashlander tribes to cooperate with House Telvanni.
The Ahemmusa, for example, are a weak tribe. Their Ashkhan has recently died, and in Morrowind's main quest, the player helps the Wise Woman find shelter for the tribe. I'd suspect that receiving protection from Aryon's guards would appeal to her.
The Erabenimsun, on the other hand, are a very strong clan. Until the player kills all leaders and instates a weakling as Ashkhan. He would be wax in the Archmagister's hands.
The Zainab almost have Telvanni blood in the chieftain's family: the Telvanni slave that the player escorts from Tel Aruhn during the main quest. Both Ashkhan and Wise Woman are thankful towards the player at that point. And if I remember correctly, Aryon initiates trade relations with them in an early Telvanni quest.
The Urshilaku finally are the most interesting tribe, at least from RoHT's point of view. When you have completed Skink-in-Tree's-Shade's first quests, talk to the other people in Tel KR, and you'll quickly catch my drift.
Twin LampsYeah, I forgot about the RoHT content for Twin Lamps. I'll probably just leave your work as is for this faction.. If I didn't have a Temple mod in mind for after Pax Telvanni I'd be more inclined to spend some time on this faction.
RoHT leaves it open to the player for what reasons (s)he may support the Twin Lamps. Either you support them, because you are an abolitionist, or you do so, because you simply want that special consulate on Ebonheart's ground. That consulate in combination with Duchess Ilmeni is the Telvanni entrance card into all-Vardenfell politics and thus to political predominance. I can definitely imagine very interesting quests emerge from this: what if the Twin Lamps realizes that they are just a means to an end? What if House Hlaalu refuses the new anti-slavery legislation? With Orvas Dren potentially out of the way, House Telvanni might use that as a pretext to seize the Dren, Ules, and Omani plantations. Lots of potential for interesting quests.
Fighters GuildI hate to pull the Hortator/Nerevarine card out too often but I have to do that here again. As such an exalted figure the PC would have a lot of sway in Vvardenfell.
I doubt that the Fighters Guild would really care for the Nerevarine title. They are an imperial faction, and if I remember correctly, only very few Dunmer belong to it. I remember them as businessmen in armor. I may be wrong, though. About
It will depend on how much time this mod actually takes me to develop once it becomes an actual WIP.
If you actually begin work on all factions, I'd schedule 5 to 6 years. I'm not joking here: RoHT took me nearly 3 years. There are days or sometimes even weeks where you can't stand to mod. Then, real life demands advertance, and before you realize, a year has gone past. And that's another reason you should let the mod grow on you: that way you'll know what's important to you and what is not.
Imperial Cult and Imperial LegionI really don't like either of these factions for a hard line Dunmer. But since the mod may be played by someone who is an Altmer, Imperial, or some other race I may do at least a bare bones content here. At the very least I'll try to make their buildings in BuUL make sense.
BuUL doesn't have to make sense (and neither do I). To me, seeing an imperial fort or chapel on Telvanni ground is plain wrong. Wolverine Hall only exists, because it is part of the armistice, and that's it. The imperial guards don't even dare venture into Sadrith Mora. They stay in their fort and try to lay low, because they know what will happen if they stick their neck out too far.
Finally, on something technical:
Would it be possible via scripting to unofficially have an NPC join a second faction?
No. The only way I can think of is to use a local (or global) variable that declares the NPC as member of a second faction. However, that variable will only work for dialogue that you have added or altered. Generic Morrowind dialogue won't be affected by it.
So, that's my 5 minutes done... Enjoy your first steps as a modder!