brian, your problem is the windshield. The 4x4's especially, the corners of the windshield tends to crack when body flexes and then it will leak, or it could just be a shitty replacement, mine does the same thing, i called a window guy, and that is exactly what he told me, said try pulling the metal frame and use silicone along the edge of windshield and look for cracks, if it doesnt work, replace windshield. I have not pulled and fixed mine, but it makes 100% sense.
Headliner leak - Check the cab corners, (part at the back of the cab on the corners where the cab is welded together) they seem to get worn out after time, either re-weld, or dabble some silicone along the spot where it is welded. Happened to my buddys truck and mine looks like it used to do it, but someone fixed when they repainted the truck.