As far as i know, there is no way to dd the roots or the kernel, but you could use dd from the PC via backupmenu for optfs, MyDocs -or simply put- complete internal card. Make sure the kernel version between N900, rootfs and optfs is the same, whichever you choose, but fastest might be nokia-kernel.
There is some info about 'building' a flashable rootfs image in the dedicated thread for backupmenu http://talk.maemo.org/showthread.php?t=63975 in the first post.

After initial flash, you would flash the rootfs image, then boot into backupmenu and restore your emmc image with dd.