Hello jon lee
What do you want to achieve? A remaster for personal use or a distro for sharing?
If a remaster, why wont a different bootloader work and forget AUFS?
If a distro there are many questions, probably all too off topic for this forum.
I will oblige somewhat.
Here is what I use in my .config;
# CONFIG_AUFS_BRANCH_MAX_511 is not set
# CONFIG_AUFS_BRANCH_MAX_1023 is not set
# CONFIG_AUFS_BRANCH_MAX_32767 is not set
# CONFIG_AUFS_EXPORT is not set
# CONFIG_AUFS_RDU is not set
# CONFIG_AUFS_PROC_MAP is not set
# CONFIG_AUFS_SP_IATTR is not set
# CONFIG_AUFS_SHWH is not set
# CONFIG_AUFS_DEBUG is not set
Possibly CONFIG_AUFS_EXPORT=y could be a good one to add. You'd be mad to add more than 127 branches except for experimentation IMHO. I only ever use 6.
Of course this all depends on initrd support AND compiling the generic linux patched with the patches from Junjiro Okajima (they apply cleanly as tested on 3.10.5), not his patched linux which makes AUFS builtin. I do have scripts for this however I will not publish them here as it is far too off topic.
Are you mounting directories or squashfs?
Ask questions on the AUFS mailing list, Junjiro is usually responsive to genuine problems.
Of course you compiled aufs-utils against the kernel headers for userspace too didn't you?