This is what I have done:

git clone git://kernel.ubuntu.com/ubuntu/ubuntu-quantal.git

git clone git://www.aleph1.co.uk/yaffs2

cd ubuntu-quantal

git checkout -b 3.5.0-21.32-yaffs2 Ubuntu-3.5.0-21.32

cd ../yaffs2
./patch-ker.sh c m ../ubuntu-quantal/

cd ../ubuntu-quantal

Ensured that kernel configuration is OK, i.e. yaffs2 is configured as module

then `make`

At the end it spits out:
  CC [M]  fs/yaffs2/yaffs_vfs.o
fs/yaffs2/yaffs_vfs.c:438:2: warning: initialization from incompatible pointer type [enabled by default]
fs/yaffs2/yaffs_vfs.c:438:2: warning: (near initialization for 'yaffs_dir_inode_operations.create') [enabled by default]
fs/yaffs2/yaffs_vfs.c:443:2: warning: initialization from incompatible pointer type [enabled by default]
fs/yaffs2/yaffs_vfs.c:443:2: warning: (near initialization for 'yaffs_dir_inode_operations.mkdir') [enabled by default]
fs/yaffs2/yaffs_vfs.c:445:2: warning: initialization from incompatible pointer type [enabled by default]
fs/yaffs2/yaffs_vfs.c:445:2: warning: (near initialization for 'yaffs_dir_inode_operations.mknod') [enabled by default]
fs/yaffs2/yaffs_vfs.c: In function 'yaffs_evict_inode':
fs/yaffs2/yaffs_vfs.c:873:2: error: implicit declaration of function 'end_writeback' [-Werror=implicit-function-declaration]
fs/yaffs2/yaffs_vfs.c: In function 'yaffs_put_super':
fs/yaffs2/yaffs_vfs.c:2506:16: error: 'struct mtd_info' has no member named 'sync'
fs/yaffs2/yaffs_vfs.c:2507:6: error: 'struct mtd_info' has no member named 'sync'
fs/yaffs2/yaffs_vfs.c: In function 'yaffs_internal_read_super':
fs/yaffs2/yaffs_vfs.c:2699:2: error: 'struct mtd_info' has no member named 'erase'
fs/yaffs2/yaffs_vfs.c:2700:2: error: 'struct mtd_info' has no member named 'read'
fs/yaffs2/yaffs_vfs.c:2701:2: error: 'struct mtd_info' has no member named 'write'
fs/yaffs2/yaffs_vfs.c:2702:2: error: 'struct mtd_info' has no member named 'read_oob'
fs/yaffs2/yaffs_vfs.c:2703:2: error: 'struct mtd_info' has no member named 'write_oob'
fs/yaffs2/yaffs_vfs.c:2704:2: error: 'struct mtd_info' has no member named 'block_isbad'
fs/yaffs2/yaffs_vfs.c:2705:2: error: 'struct mtd_info' has no member named 'block_markbad'
fs/yaffs2/yaffs_vfs.c:2729:11: error: 'struct mtd_info' has no member named 'erase'
fs/yaffs2/yaffs_vfs.c:2730:11: error: 'struct mtd_info' has no member named 'block_isbad'
fs/yaffs2/yaffs_vfs.c:2731:11: error: 'struct mtd_info' has no member named 'block_markbad'
fs/yaffs2/yaffs_vfs.c:2731:34: error: 'struct mtd_info' has no member named 'read'
fs/yaffs2/yaffs_vfs.c:2731:48: error: 'struct mtd_info' has no member named 'write'
fs/yaffs2/yaffs_vfs.c:2733:11: error: 'struct mtd_info' has no member named 'read_oob'
fs/yaffs2/yaffs_vfs.c:2733:29: error: 'struct mtd_info' has no member named 'write_oob'
fs/yaffs2/yaffs_vfs.c:2754:11: error: 'struct mtd_info' has no member named 'erase'
fs/yaffs2/yaffs_vfs.c:2754:26: error: 'struct mtd_info' has no member named 'read'
fs/yaffs2/yaffs_vfs.c:2754:40: error: 'struct mtd_info' has no member named 'write'
fs/yaffs2/yaffs_vfs.c:2756:11: error: 'struct mtd_info' has no member named 'read_oob'
fs/yaffs2/yaffs_vfs.c:2756:29: error: 'struct mtd_info' has no member named 'write_oob'
fs/yaffs2/yaffs_vfs.c:2946:2: error: implicit declaration of function 'd_alloc_root' [-Werror=implicit-function-declaration]
fs/yaffs2/yaffs_vfs.c:2946:7: warning: assignment makes pointer from integer without a cast [enabled by default]
cc1: some warnings being treated as errors
make[2]: *** [fs/yaffs2/yaffs_vfs.o] Error 1
make[1]: *** [fs/yaffs2] Error 2
make: *** [fs] Error 2

Jarl