A Question on Modding Morrowind

Pretty much, you have to wait for Corprus to get to day five when you become like those newly infected with it and not like the Lame Corprus people. You become super slow and when you go to Dagoth, he makes you into an Ash Zombie and works you up to the Rank of Ash Vampire with the title of Dagoth Nerevar. After doing quests for him and all of the Ash Vampires and even dominating the Ash Vampires (making you effectively the Dragon to Dagoth), you then are tied back into the Main Quest by speaking with Caius again, where you can choose what to say to him. Where it diverts is after becomming Hortator and proclaimed Nerevarine by the Ashlander Tribes. Then when speaking to Dagoth once more, he asks you to get Wraithguard from Vivec, in which Vivec decides to go ballistic and try to kill you. From then on, you need to end him and get Wraithguard to work "The backpath way", and after doing so, Dagoth will ask for the tools of Kagrenac in which you get the option to help him or betray him.

Perhaps the only problems I had were getting to Dagoth Ur, getting around as an Ash Zombie and perhaps getting Vivec's notes out of Vivec's secret library. In Corprus Infected form, you can't move fast at all, so I used a cheat (coc "Dagoth Ur, Facility Cavern") to get to him. He then helps you get up from there, teaching you how to use new forms and stuff. The most annoying was the Ash Zombie due to being effectively blind (100% non disspellable), so I used cheats to get around because he wanted the Character to talk to the Ash Vampires. Once able to see again though, it wasn't a problem.

As for Vivec's Secret Library, you're supposed to look for pieces of paper detailing things. 3 of them are easily found, either behind a leaning book, atop a bookshelf or on the table being written. The last one was hard to find, but just to note it, it's right underneath some book on the bottom shelf of the left most shelf if you were facing them.

I would recommend NOT going back to Caius until Dagoth tells you to and you are able to revert back to a human form (You can change from Ash Vampire to human by Dagoth giving you your own artifact). And when you do, don't worry if he attacks you and you must kill him. The one message "Broken chains of fate yada yada reload save or continue in broken world" will pop up for him and for Vivec should you decide to kill him too, but it's fine either way since Caius was supposed to disappear after getting info on the dissident priests and Vivec can just attack you if you're on Dagoth's Side.

I pretty much stayed on Dagoth Ur's side. Don't like the idea of being the Emperor's little proxy as well as perhaps seeing from Dagoth's point instead.