If the shaft went into the trans easily, then it should come out just as easy as it went in. Thing is though, that clip at the end was probably not as rounded as the original. You need to use some persuasion to remove it. As in, mother of all daddy'* pry bar'*.
You don't need the spare tire cover. The parts store should have asked you if you were naturally aspirated or supercharged. The supercharged engines have a different size shaft(beefier).