You'll just need to check each possibility, as noted above. Each wet spot can have more than one possible source, so it needs to be eyes & hands on, tracing backward.
My culprits were mainly sunroof and windshield seals, with clogged rocker drains. Sunroof seal leaked, overwhelmed the drains & thus tray, water made its way on top of the headliner, and mostly came down the a-pillars, making its way to the floor on each side. I also had some water running back to the rear passenger corner, getting the floor wet there. The windshield also dripped at each corner.
Cleared the tiny rocker drain slits with a small paperclip, and dirty water came gushing out. I then rerouted the front drain hoses through the holes in the floor, just behind each kick panel trim. Draining into the rocker panels is not a great design IMO. Resealed the windshield, and went ahead and sealed the sunroof as I never need to open it, and disconnected the wiring for the motor in the map light assembly.
When you check the roof rack mounts, also inspect your roof paint for any signs of cracking or otherwise. I had a couple spots to touch up, and found a couple tiny pea-sized holes in the metal, where there was a little spider cracking in the paint. Ground to clean metal, patched, repainted. After all those things, never had a single drop of water intrusion again.