Originally Posted by Phorize
I built an initrd.gz (using output from mkinitrd_command_generator.sh)-it installed to /boot
In my experience, mkinitrd_command_generator.sh doesn't usually give very good advice (well, it probably does on very standard installations, but I have always had to modify the suggested command due to encryption and other funny things).
Based on your post I would guess that the correct command could be
mkinitrd -c -k <your kernel> -m <all colon separated modules you need, especially your root filesystem> -f <your root filesystem> -r /dev/crypt/root -C /dev/sda3 -L -u
You may also try to move your kernel and initrd.gz to the EFI partition and adjust the elilo.conf accordingly (perhaps it's not necessary, I don't know whether elilo can look to other partitions with different filesystems directly but it's where I have my boot data and all works well).
Hope some of this helps you