I managed to fix the issue by doing the following with each disk: (I use X here 
to represent the disk.)
mdadm --manage /dev/md0 --fail /dev/sdX1
mdadm --manage /dev/md0 --remove /dev/sdX1
mdadm --zero-superblock /dev/sdX
mdadm --zero-superblock /dev/sdX1
dd if=/dev/zero of=/dev/sdX bs=1 count=2048
fdisk /dev/sdX (recreated the first partition and mbr on each disk and ensure 
type set to fd)
mdadm --manage /dev/md0 -a /dev/sdX
(Allow the array to resync to 100% before doing the next disk. Each resync took 
a few hours.)

Once I had done this for all of the disks in the array I rebooted to the
latest kernel 2.6.35-28-generic-pae. On the first boot I still had the
same problem so I stopped the array with mdadm --manage --stop /dev/md0
and made the following changes to /etc/mdadm/mdadm.conf

DEVICE /dev/sda /dev/sdd1 /dev/sde1 /dev/sdf1 /dev/sdg /dev/sdc1
ARRAY /dev/md0 level=raid5 num-devices=3 
UUID=726e3b03:242ebdf0:85c68096:6992ccf3 

I then restarted the array with:
mdadm --assemble -c /etc/mdadm/mdadm.conf /dev/md0

Then I updated all of the initramfs modules:
update-initramfs -k all -u

When I rebooted my array came online automatically without errors.

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https://bugs.launchpad.net/bugs/797174

Title:
  Ubuntu 10.10 2.6.35-28 kernel does not assemble md devices correctly.

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