Have some one watch the roof while you push up on the sunroof pans from the inside to see if they lift up from the roof , if they do the outer frames need resealed to the roof. The rattle might be from the through glass mounting screws being loose. Check them with a T driver for looseness, they also allow for alignment. Reseal the plastic drain cups to the metal pans, the factory sealant is s**t! BTW the factory glued the drain hose to the brittle plastic drain tubes on the frame. Button up inside the truck and have your better half spray the crap out of the roof with the water hose while you look for leaks.
I covered my inner roof metal with foil backed sound deadener. (AKA Roll of Adhesive Flashing from hardware store). Then 1 to 2 layers of the mylar bubble wrap insulation taped/sealed in with alu. duct tape. I get zero radiant heat transfer on the few sunny days since, should be easy to heat n cool now. It's also really damn quiet too!! ( I also did all 5 doors with the sound deadener)

 

While the headliner was out, installed new drain corners, added wiring and insulated the roof.