I have this problem with my TF Cool Blue, because I have the glass rear window it is impossible to fold the wind stop down with the hood up. I don't have the tools to be able to modify the wind stop as in this excellent tutorial so I modded mine to be able to quickly fit or remove it by simply slotting the holes in the brackets.
I did tidy up the cuts after I took the after cutting picture. Also due to my head height when driving lowering the height of the top bar of the wind stop would obstruct my rear view a little.