Can't Interact With Some NPCs/Quests?

[SmeggingTosspot]

Whenever I go into Whiterun I can't talk to a lot of the NPCs, especially the shopkeepers or the Jarl. I used the console command 'unlock' on the front gate of Whiterun when it was locked by key (I had never encountered that before). At first I just thought "Oh well, I'll just avoid Whiterun" But now I'm doing the Imperial's questline and I have to deliver something to the Jarl for General Tullius (By the way, no quest pops up for that, he just tells me to go there and the last quest ends). When I go to talk to Jarl Balgruuf, It's as though he's a villager. No dialog options pop up, he just says "Aye," "What it it?" and things like that. I have a mod for an alternate beginning of the game, so I never had to go warn Balgruuf about any dragons or anything, so I don't have the quest for that either.

Things I've tried doing to fix it so far:
- Verify integrity of game cache

- Using the 'setstage' and 'startquest' console commands. (When do these nothing happens, just some textwall filling up the console, and nothing after that.)

 

I'm worried that if i uninstall mods to try this I wont be able to get the materials from the mods back :S

Thanks for your time! I really hope someone can help me out with this as I've recently started liking Skyrim again.