It's actually pretty weird. You have to "buy" the game again. Rechoose the game on the store, when it asks you to pick your version you'll have to choose the FREE one, which will put you through the whole checkout thing again. Then when the window with your choices popped up(the one you saw at first with both games and the VITA online pass) the alternate costumes will also be there. I'm not sure why they weren't there at first, but this worked for me.
Go to the psn store go to the psabr page choose free or (version) when you are on that page choose the free option i think it is about 7.2 gb) checkout -> confirm purchase then it should be available in your download list.
it should be able to download man! if it doesn't work redo the process all over again if possible ,if you order in psn store you should have the ---> the theme,online pass,psvita version,ps3version,skins