apt-get update mdadm scary warnings

All you need to do is:

First, change the mdadm.conf with the result of mkconf

/usr/share/mdadm/mkconf > /etc/mdadm/mdadm.conf

Then, you have to update the initramfs

update-initramfs -u

Now, you can reboot the system.

Looks like the warnings are correct - your current layout differs wildly from your mdadm.conf.

The settings that it's given in /usr/share/mdadm/mkconf appear to be correct. Just to verify - do your /etc/fstab entries match up with your current mounts?

Since something large-ish seems to have changed on this system, I'd still be a bit concerned about the reboot. Back up first!