Hi there is there anyway to manipulate the verticies manually if they don't want to align?
In the UV Editor select the Vertices that you want straightened out (one edgeloop at the time!) and press SHIFT+W > Align....
But that is a pain if you want everything straightened out. Follow Active Quad should work; make sure everything is selected when you try that.
Like spikeyxxx mentioned, you can go ahead and utilize the Follow Active Quads method as explained at timestamp 15:50. That should normally get you most of the way!
However, if for some reason that doesn't seem to be doing the job, you can manually edit UVs like you would a mesh. Make sure you are in Vertex selection mode in your UV editor (top left corner) and you should be able to move any vertex you'd like. :)