When I reach Esbern in the ratway he is silent, I mean he just stands there and says nothing. But I can still speak with him and all the dialogue choices are there, it's just he's silent and doesn't open the door for me.

Go to http://www.uesp.net/wiki/Skyrim:A_Cornered_Rat page and scroll down to the Bugs section. There are a couple of things you can try with the ini.

Thank you, Yasgur. As soon as I made this topic I checked that same page, lol. Everything is working now....phew.