Out of curiosity have you looked into booting nemo via a chroot ala nitdroid? I briefly tried to get it to work that way, but at the time I was trying to make a single kernel that booted both Nitdroid and Nemo, but ran into some issues and lost interest. Your way of actually separating the kernels is a lot better, and I think not having to sacrifice a partition on the EMMC would be a better solution to running Nemo. You could basically add something like a real_root argument to the kernel command line, and the preinit script could take that and use it to determine where to chroot before running init.