Bolts may look good, but are they sealed. I've used 3M seam sealer, in/on threads/bolts
Pour/run water in rain channel around bolts/mounts. Do with vehicle front high, so water runs back one side at a time. Isolate so water going around specific areas.. Do windshield next, than rear hatch or in any order that works for you.
I use a 6mm guidable borescope, to look up under headliner. Helps isolate.
Additional: Pressurize cabin with blower, HVAC fan set to full speed, set outside air. Soap or glass cleaner bubbles, can be revealing.
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