I believe most of it is indeed from Malick, but “Is the body of the wise man, or the just, exempt from any pain? From any disquietude, from the deformity that might blight its beauty, from the weakness that might destroy its health?” is adapted from Augustine (City of God, XIX.4) and the following is a quotation of Kierkegaard (Four Upbuilding Discourses, IV.19-20):

“The very moment everything was taken away from Job, he knew it was the Lord who’d taken it away. [...] Does he alone see God’s hand who sees that He gives, or does not also the one see God’s hand who sees that He takes away? Does he alone see God who sees God turn His face towards him? Does not also he see God who sees God turn his back?”

The scene of the arrival of the telegram is nothing but an “Annunciation” filmed from “grace” to “gravity”.
“Steve” is the diminutive of Stephen. Malick was a pupil at St. Stephen’s Episcopal School (Austin, Texas). You should really pay attention to Steve, his relation with RL, his father, mother and, most of all, death.
R.L.: definitely “River of … Life, Love, etc.”: RL is continuously associated with the river (and the waterfall).
The stained glass alluded in the previous post is an “Ecce Homo”: this very precise episode of the Passion has more than religious associations.
For understanding the scene with the boys playing at the window before leaving the house:
“Two prisoners whose cells adjoin communicate with each other by knocking on the wall. The wall is the thing which separates them but is also their means of communication. It is the same with us and God. Every separation is a link.” (Simone Weil)
The alligator you see in the baby’s arch: it is an animal associated with the power of God in the Book of Job.
That “He was in God’s hands all the time” was inspired in Lewis (A Grief Observed). Maybe you already knew that…
The bridge: the “re-ligare” clue is a false one. You see a bird flying along the bridge:
“As the forest bird crosses the peaks in flight,
Over the river shimmering past your floats
Airy and strong the bridge,”
(From the poem that structures the film.)

If you want to understand what “door” is that, you must first understand who the woman on the other side of it is.
Last advice: don’t try to “understand” a film that took 30 years to make in just 3, 4 or 5 viewings. I needed much more than 10.

If you want to consider this in a more profound way:

http://reviewingtreeoflife.blogspot.com/

Some knowledge about cinema necessary (some patience and open mind too).

Soul crushing is about the sum of it actually…and if it doesn’t crush or if you try not to live with it and just talk it away then well…I am not sure it is worth being called Christian considering it’s about a God who got crushed too.