In the Clockworks Court, the area outside the mansion, head to the right of the entrance to the mansion and keep walking along the railroad track. Once you hit the end, use the Dark-Light Device to reveal a hidden chest with the first gem inside.
The Warehouse is full of rolls of string, and each one can be taken to the spindle to be unrolled. Use the Dark-Light Device to find a hidden green spindle with the second gem inside towards the back of the Warehouse. Arrows on the floor should help you find it.
Just as you enter into the left side of the Clocktower Gate, use the Dark-Light Device to reveal a chest with the third gem inside.
After getting thrown down into the Storm Cellar in C-2, yank off the cloth hiding the portrait above the bed. Use the Dark-Light Device to reveal the fourth gem.
Just before moving onto the next room in Canyon Hall, take a left and you should find a small area with a door. Enter it to find yourself in the Canyon Stairs. The fifth gem is above the middle of the stairs in a spider web.
In the Quarry, you will be tasked to yank back the mine cart four times to progress through the mission. Tug on the rope two times to get the mine cart out of the hole its in. Enter that hole and you should find the sixth gem in a spider web.
Enter the Clockmaker’s Chambers. Suck up the rug and use the fan to change the time of the clock to 9:00. This will set off the alarm, causing the Greenie to wake up. Defeat him and grab the seventh gem.
Once you make it to the upper level of the Roundhouse Pit, cross the set of beams to make it to the other side. Instead of going through the door that leads to the Transportation Hall, cross another set of beams that take you to another area with the eight gem waiting inside a chest.
As you make your way to the Ancient Poltergeist in the Roundhouse Pit, walk down the stairs and walk past the brick wall to reveal a small section with the ninth gem inside.
At the bottom of the Gear Chamber, use the Dark-Light Device to restore a missing bridge. Walk up the pathway and into the wall where a door can be found. Enter it to be warped to an alternate dimension. Luigi will have to collect all the Red Coins before the time limit to earn the tenth gem.
In the Maintenance Hub, jump off the giant cog to the sandy bottom and use the Dark-Light Device to reveal a hidden chest in the front of the area.
With Yellow Toad at your side, head back to the Service Elevator where his Pixelator waits. Before sending Toad off, suck him up into your vacuum and blast him to the other side of the room. Toad will grab the twelfth gem and use a spring to get back.
Once you finally make it through the Clocktower Gate, head to the left when you are in Movements. When you get to the window, the camera will pan around and show you the thirteenth gem resting in the sand. Suck it out and grab it to complete all the gems in Old Clockworks!