To obtain invisible Zeke, you must hold down ABLR as soon as the GC logo dissapears. Hold this down until the Title screen and open your game file like you normally would. Make Zeke face you and you will only see his clothes!!
To play as Skeleton Zeke, You need to hold down ABXY as soon as the GC logo dissapears until the title screen and you can now play as Skeleton Zeke (Just start playing like you normally would and observe Zeke as you play.)
pause the game hold down-right on the d-pad and hit BXXX BXYA and then unpause........thats it you won't lose anymore health nor gain any.......
To get Level Select, hold down right on the D-pad and press XXBYYBXA to obtain Level select on the pause menu.
Hold down right and press BBYYXXXA to upgrade your weapon