I've had my hard top leaks and my door rattles resolved. Hopefully...
The top issues I dealt with myself. After having all 3 parts off the jeep, I cleaned all of the gaskets and their mating surfaces and reassembled everything. Some folks are using various gasket dressings like silicone or armorall. Every time I take the front 2 panels off, I clean the gaskets and reinstall. No more leaks!
The rear window leak has more to do with water and dirt getting between the glass and gasket at the top. If it's clean and dry, no leaks. If you open it while it's wet, then it seems that the seal is broken and water seeps through and runs down the window. Just another P. I. T. A. Jeep thing!
Have your dealership replace the door latches with the "revised" latches and your rattles will be gone! (There's another thread on here about that one!)