Tell us how your Linux partitions are used now.
dd is a bad idea because it copies all the underlying filesystem metadata, so if you copy a small partition onto a bigger partition the extra space appears to have vanished. Copying a bigger parttion to a smaller one .. don't ever do that as some the bigger partition will be left behind.
You should copy files from one parttion to the other but boot with a CD, so your normal gentoo root filesystem is not live. This avoids the complications with copying /dev /sys and /proc, which are not real filesystems.
Book your CD, mount the donor partition to /mnt/gentoo.
Mount the copy to /mnt/floppy (any mount point will do as long as its not inside /mnt/gentoo)
Now use the
cp -a /mnt/gentoo/ /mnt/floppy/
to do the copy. Read
while it runs.
If your want to be able to boot the copy, your will need to edit /etc/fstab (in the copy) and grub.conf as your (real_)root=/dev/... will have changed and possibly your root (hd... too.
The MBR does not belong to any filesystem or partition, so operations on partitions or their filesystems will not harm the MBR.