You should be able to get 2 of the 3 God Bumpers in any playthrough (Museum after beating all Gauntlets & beating Champion). The 3rd doesn't appear ingame, much like how YuGiOh Sacred Cards (gba) never actually lets the player use The Winged Dragon of Ra (and I never found a good place to put the last God)
Glad you had fun :) What was your team for beating the Champ?