my 90 had the same problem after my car was lightly rear ended and had the trunk LID mounted lights replaced. the knock-off non Honda tail lights will leak like a sieve. Tightening the bolts that hold the lights to the trunk lid will help some, as will clear silicone gel (at walmart for about $3.00).
as far as the passenger floor being wet, check the weatherstripping on the door, as the spray from the wheel going down the road will get in there and make the carpet actually squishy. replacing the weatherstipping there will solve the problem, as did with my 90 EX coupe.
If all else fails, check around the moonroof (as previously suggested) and around the front and rear windows (as previously suggested with a water hose).
good luck