Well welcome to the world of task force. It very inherent for this model especially where seals are gone.
It will come in around the door, in from the cowl vent which runs down the sides. Kick panel leaks. Hinge areas on doors. Mine currenly has a drip with heavy rain in from the wiper shaft going in thru the outer sheet metal since a rubber piece went bad. Its the main reason the floors and runners on the these trucks are toast. Lots of guys that start modifying their trucks like putting in smoothies for the cowl. removing vents and sealing up the kick panels good and making sure the door rubber is good and tight can keep the water out. But you should keep a yearly eye on your seals and you can stay ahead of it.