A bit more on this: there are extended interviews as bonus features on the Heaven Adores You DVD, and there is a specific section on 'The Songwriting Process'.
In short, Larry Crane, Joanna Bolme, Sean Croghan(sp?), Pete Krebs, et al talk about some of the things I mentioned above. They also say how sometimes he would play and write music endlessly in big chunks, and that the lyrics would come later (having been on tour or something). Conversely, he would also write lyrics for ages and ages without any music, and that would come later. They also mention how he would commonly recycle old ideas, and they mention his high school bands and music.
Hope that helps!
Get the DVD!