Okay well basically I am pretty close to the end of the main quest, I think. I just sat down with everyone at High Hrothgar and had the peace council and by the sounds of it, the civil war is over. So basically what I want to know is if after this point, can I still choose a side and finish the civil war quest line? Quick responses would be appreciated

The truce is only until the dragon crisis is over. After the main quest the war continues.