Actually, all of the dungeon Gold Skultullas are in different places in the Master Quest, not just in the two dungeons you mentioned. First, we need to know where the Skultullas you missed are located. You can check each dungeon (this includes the Ice Cavern and, although you already checked it, the Bottom of the Well) to see if you got all the Tokens the same way you checked the well and the Shadow Temple (the Gold Skultulla icon next to the dungeon name on the map; if there's no icon, you missed at least one Skultulla in that dungeon), and you can check the overworld locations like Kakariko Village by checking your overworld map and displaying the name of each area; look for a Skultulla icon next to the location name just like the dungeons. If one of the ones you missed is NOT in a dungeon, remember that all the non-dungeon Skultullas are in the same place in Master Quest as in the regular version, although everything is mirrored (for example, the Skultulla on the wall in the Graveyard is still on the wall, but because everything is reversed, it's on the opposite wall). Once you know what area the missing ones are in, let us know and we can help further.