Once I finish the main quest and it says "2 weeks later" Elder Lyons is suppose to come in and talk to me, but instead just walks back and forth out in the hall, how do i fix this?

Try reload a save.

I have 3 times, 2 different saves.

Is there an advance quest code i can put in the console?

You're lucky to find him when you wake up. Unlike with me he's never there when I wake up, instead I have to go find him. But mine's mod-related as with nothing but the DLC's loaded he's standing in front of me.

With yours, can you select him to talk to him? Even though when you wake up he is supposed to force-greet you, you should still be able to talk to him first.

No, when I wake up, I can't move, and he stays in the hall walking as far as the door then turning and walk back to the right of the room in the hall and then he turns around and walks back as far as the door again, then repeat.

I've now tried making Falwks and the chick put in the code, and i get the same out come, when I wake up, I cant move and he stays in the hall.

You're on the PC? If so, open the console and type enableplayercontrols that'll allow you to regain control of your character so you can move and go over to him. Even if he won't force-greet you you should still be able to select him to talk to him.

Thanks I'm able to continue now.