If the holes are directly in the floor these are drains in case of flooding , srping cleaning etc. If the holes are on actual frame these are refrence holes for frame tech to hang guages for frame repairs. Any drains in fenders are probally for drains from your cowl vent . Your cabin wettness could be anything from a leak in windshield to leak at firewall. Get friend flashlight and water hose out to detect were water is entering. Start a gentle flow of water at top of windshield and work slowely around while someone is inside close up searching for leak. After windshield check inside firewall inside engine compartment. Work this from one side to other. Also check drains from cowl vent area. ,and check drains from sunroof if u got 1 . Cowl vent drains and sunroof drains can be blasted with compressed air. Check inside sunroof are for these drains. If you don`t have a air compressor maybe a friendly shop near by would do this for u . Good luck and God bless P/s Auto body sealer for fire wall area and silcone sealer for small leaks in windshield.