I think to fight Phunbaba a second time you have to go to a secret room behind a bookshelf in the town you found her the first time. Or I might be confused with the way to initiate the first fight.

You dont get to have shadow at the end but its still fun to see all the dreams anyway.

Im pretty sure they tell you that you can head to kefkas tower after you get the airships and there are enough clues that lead to each other within the sidequests to tell you where the other characters are.