I do remember reading that he really liked what Lynch did with the Guild Navigator, though he thought it could have been "stranger." Don't recall ever hearing that the movie influenced the last two books, though I suppose it's possible as they were both being written around the same time.
RE characterisation: It's funny, but I remember thinking that Paul never quite seemed like a "real" person until after he became the Preacher. Oddly enough I felt the same thing happened with Alec Newman's performance in the mini-series. He really came alive as the Preacher.