Lyric discussion by Knife2aGunFight 

I'm not absolutely sre these lyrics are correct."we build her with" line specifically.

anyway I'm not exactly sure but judging from all the referances to Gardening and plant life I would say the entire album catalogs a person who is losing their Faith in God because God has been vengeful (Messes of Men, Nice & Blue Part 2) for his evil deeds (adultery, gambling) but by the end of the story the character finds there is nothing left BUT to have faith(In a Sweater Poorly Knit) The Spider tracks are the order, as the plant(faith) is dying.

I could be very wrong though I need to analyze all of the corrct lyrics, but that's my first impression.

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