While you're looking for leaks be sure to check the caulking in the rain gutters above each door.
Cowl drains frequently get plugged with organic debris that divert flow into the cab. (I've pulled these rubber boots completely out)
If you have the interior removed you might want to start at the bottom (lowest spot) and pour a cup of two of water, then go look and see if it appears inside.
Jim,
Lil'Red is a '87 F250 HD, 4.10's, 1356 4x4, Zf-5, 3G, PMGR, Saginaw PS, desmogged with a Holley 80508 and Performer intake.
Too much other stuff to mention.