Here is the list of code that has been possibly incorrectly dropped in the x86_64 port.

arch/x86_64/kernel/sys_x86_64.c
code in mmap to check the MAP_MIGRATE flag.  The base code is rather different so I'm not sure how to deal with this yet.
arch/x86_64/lib/csum-wrappers.c
csum_partial_copy_from_user - cope with remote user process
arch/x86_64/tools/offset.c
Definition of thread_rsp0 - used in ret_from_rproc in entry.S

Not needed any more, ret_from_rproc has changed.
A whole bunch of stuff in arch/x86_64/ia32.
Probably only relevant for 32bit libcluster.  To be done later.