Any poly used for floors is suitable. Varathane, minwax, etc. all make one for cork floors.
If you need to sand it, then you can use 150 grit. I don't recommend going any more coarse unless you are ready to do some serious sandings.
if you find areas that need to be filled, you can take some cork dust and mix it with some poly and fill the areas. yes, it will be noticable, but any area that has been ripped open will be noticable. unless you can find a match of the floor tile, then you can try to cut out the part that is damaged and replace it with the new tile. obviously, do this before putting down your finish.