By mixing spiritual blurbs ("You seek problems because you need their gifts") with events in the story meant to convey a particular lesson, Bach attempts to explain our own nature and the nature of what we call "God".
The picture of "God" here, is essentially that which mystics of all spiritual paths (including Christian mystics) seem to arrive at, ie.an all-encompassing consciousness that is beyond description and can't be anthropomorphized in the way that we love to do. Donald refers to this God as the "Is". This particular idea is addressed in passing several times but not harped on (what purpose is there in trying to describe something that can't be described).
The picture of humanity is the main focus and Donald tells us that we are all our own Messiahs, that we are all gods but have just forgotten that fact. Thus, our spiritual challenge is to transcend the illusion of our current physical situation and reclaim our true spiritual identities.