I was able to get the open files changed to 65535 using the above link. Today after I started my computer I got the same error I've been getting about not being able to create a new thread. 

~$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 31429
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 65535
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 31429
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

Error I see when the backup runs automatically.

Traceback (innermost last):
  File "/usr/bin/duplicity", line 1555, in <module>
    with_tempdir(main)
  File "/usr/bin/duplicity", line 1541, in with_tempdir
    fn()
  File "/usr/bin/duplicity", line 1393, in main
    do_backup(action)
  File "/usr/bin/duplicity", line 1472, in do_backup
    restore(col_stats)
  File "/usr/bin/duplicity", line 728, in restore
    restore_get_patched_rop_iter(col_stats)):
  File "/usr/lib/python2.7/dist-packages/duplicity/patchdir.py", line 558, in Write_ROPaths
    for ropath in rop_iter:
  File "/usr/lib/python2.7/dist-packages/duplicity/patchdir.py", line 521, in integrate_patch_iters
    for patch_seq in collated:
  File "/usr/lib/python2.7/dist-packages/duplicity/patchdir.py", line 389, in yield_tuples
    setrorps(overflow, elems)
  File "/usr/lib/python2.7/dist-packages/duplicity/patchdir.py", line 378, in setrorps
    elems[i] = iter_list[i].next()
  File "/usr/lib/python2.7/dist-packages/duplicity/patchdir.py", line 107, in filter_path_iter
    for path in path_iter:
  File "/usr/lib/python2.7/dist-packages/duplicity/patchdir.py", line 121, in difftar2path_iter
    tarinfo_list = [tar_iter.next()]
  File "/usr/lib/python2.7/dist-packages/duplicity/patchdir.py", line 339, in next
    self.set_tarfile()
  File "/usr/lib/python2.7/dist-packages/duplicity/patchdir.py", line 333, in set_tarfile
    self.current_fp = self.fileobj_iter.next()
  File "/usr/bin/duplicity", line 765, in get_fileobj_iter
    manifest.volume_info_dict[vol_num])
  File "/usr/bin/duplicity", line 808, in restore_get_enc_fileobj
    fileobj = tdp.filtered_open_with_delete("rb")
  File "/usr/lib/python2.7/dist-packages/duplicity/dup_temp.py", line 120, in filtered_open_with_delete
    fh = FileobjHooked(path.DupPath.filtered_open(self, mode))
  File "/usr/lib/python2.7/dist-packages/duplicity/path.py", line 779, in filtered_open
    return gpg.GPGFile(False, self, gpg_profile)
  File "/usr/lib/python2.7/dist-packages/duplicity/gpg.py", line 224, in __init__
    'logger': self.logger_fp})
  File "/usr/lib/python2.7/dist-packages/duplicity/gpginterface.py", line 374, in run
    create_fhs, attach_fhs)
  File "/usr/lib/python2.7/dist-packages/duplicity/gpginterface.py", line 420, in _attach_fork_exec
    process.thread.start()
  File "/usr/lib/python2.7/threading.py", line 736, in start
    _start_new_thread(self.__bootstrap, ())
 error: can't start new thread