Theirs many possibility's that is causing your rattle!
1) Aged Sunroof Seal (#15 in Picture) will allow the Glass not to seal to the body of the truck , Wind noise and rattles can come from this.
2) Their are 2 plastic covers (#7 in Picture) that are attached to your Sunroof Rail Guides and Sunroof Metal Frame that are designed to hide the torx screws which holds the Sunroof Glass Frame to the Sunroof Assemble. These Plastic Covers if not attached properly will rattle too.
3) When your sunroof is open to the vent position, attached to the sunroof rail guides at the opening of the rear of the roof is what is called a Drip Tray (#4 in Picture), The Drip try is designed to catch water run off from the Top of your Roof Opening when your Sunroof is open to Vent. Their are 2 Screws Per Side that attach the Drip Tray to the Sunroof Rail Guides, If either of these screws are loose you will also get a rattle. It would be Metal on Plastic.
4) Their are 4 Sunroof Panel Clips that hold the Sunroof Sunshade to Sunroof Rails, If any of these are Missing or Broken you will get a rattle.
If you contact me i can walk you through a process over the phone to help you find your problem, If I can help you in any way just ask.