First off - The dragon randomly falling from the sky, and not being soul-svckable, I can live with that. Its an annoyance, but doesn't block anything.

The main problem I am having is that I have just finished Alduins Bane quest.

However it never triggered the next quest to talk to Arngeir, Para or the other dude.

SetStage didn't let me trigger the next quest, I had to make a mod and then set the quest flag to be non-run-once.

Then I was able to do SetStage to trigger the quest.

Unfortunately, every quest after that point, has required setstage and a mod to unset the run-once flag.

In addition, the NPC's involved in the quests don't want to discuss the active quest.

Eg: The quest says - Talk to Parathurax, I talk to him, but all he offers is to let me meditate on a Word of Power.

This issue occured earlier in my game - with the Grey Beards, Arngeir would refuse to move to the main room, and I was unable to learn the 3rd word of Unrelenting force.

I had to use SetStage to get past the quest and do Disable on Arngeir and make a new actor for him.

Anyone have any ideas on how to solve this?

I have a good load of mods installed, but I am hesitant to remove them all.

Another symptom I am seeing is that occasionally I get stuck in Conversations, I have to wait for about 1-2 minutes for the conversation to progress to the next stage of dialogue.

Eg: Tab doesnt exit, clicking or button clicks don't move to next dialogue, Esc doesnt work either.

That is likely the issue. A mod is messing something up. What i recommend is disabling them all (just uncheck them) and either load a save or start a new game.

Don't overwrite any current saves while doing this. This is just for troubleshooting. See if the issue goes away. Then check them a few at a time.