New RAID array will not auto assemble, leads to boot problems

Two issues spring to mind

  1. You've got duplicate array definitions in mdadm.conf. Replace (or comment out) the block of three lines following # definitions of existing MD arrays so that each array is declared by your most recent scan.

  2. A typical scenario for RAID arrays that fail to build on boot is that either they have not been updated in the initramfs or they are not set to run at boot time. A really quick scan through the guide you referenced doesn't appear to mention these steps, but I could be wrong. On Debian systems the commands are:

    dpkg-reconfigure mdadm    # Choose "all" disks to start at boot
    update-initramfs -u       # Updates the existing initramfs