I had a similar problem, water ran from the top of the passenger side into the back passenger corner of the interior and dripped down onto my speaker and onto the floor. What I did to "fix" it is just use black electrical tape and put at the top of the door, above the rubber part. It hasn't leaked since so that did the trick for me.
If yours is leaking into the front of the cab, not the back like mine, I really am not much help. All I can say is that I just took of the plastic interior parts and felt up to where it was wet. If you are able to do the same I would give it a shot.
I only cheaped out cause I took it to Ford repair bay and they thought my whole back window was once wrecked and wanted me to buy a whole new window.. glad I never.
2008 F-150 Supercrew Lariat 4x4, 5.4L.
2007 Ranger Supercab FX4, 4.0L, Accident mod done in December, 2012, totalled.
1998 Ranger Reg. Cab, 3.Slow. Sold, then totalled.