First of all, Welcome to the forum
Now the leak with the windows, yes many have had issues. most were fixed with a window adjustment. The door panels need to be removed and the adjustment happens behind the panel. (try a search for window leak, or Mac Haik of Houston, They did the work for Houtex and have helped other dealerships)
Second the bed leak, check out this thread to see it will help you
My 05 SSR truck bed water leak solution