Super Gem 1: Inside a hard-to-miss alcove at the last of the three Touchstones leading to the first Flip Panel.
Super Gem 2: Just before the second Clear Pipe Cannon, Captain Toad must enter the door. Once outside, Captain Toad must then follow the Flip Panel to the Donut Blocks that the Super Gem rests upon, then get out of there.
Super Gem 3: On the Touchstones just after the second Clear Pipe Cannon. To get it, Captain Toad must enter the door, then move the lower Touchstone to the left to access the Super Gem.