Setting the super-minor on the superblock of the array didn't seem to have much affect (from what I can tell it wasn't even being written). The solution is to specify the UUIDs of the arrays with the device names you want in your mdadm.conf. Here's what mine looks like:
dknowles@bender:~$ cat /etc/mdadm/mdadm.conf | grep ARRAY
ARRAY /dev/md1 level=raid1 num-devices=2 \
UUID=6e5ff2ae:5724fb93:a0a0eea7:e933aaa5
ARRAY /dev/md0 level=raid5 num-devices=3 \
UUID=40a6c7b8:76b2e648:a0a0eea7:e933aaa5
ARRAY /dev/md2 level=raid1 num-devices=2 \
UUID=e4977645:8fd7f50c:a0a0eea7:e933aaa5
Presto! Now from a cold boot, all the drives are detected normally. Which is good because now my backup cron will stop sending me error emails every night. On to the next, more interesting problem in my life! :)
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