The stock speaker grill just pry up on one side and then slide out. The speaker boxes are then attached with two screws. Undo those, push down and slide out the boxes come out. There is also the small electric connector to remove.
5" speakers could fit if you did some surgery. I put 4" speakers in. Originals were 4 1/2". Of course, you can make your own boxes and do what size you want.
Now, as far as the package tray itself is concerned, it is a part of the car and I doubt is removable.