Assuming your S4's IP address was say 192.168.1.99:
ssh -l root 192.168.1.99 (or equivalent with putty)
wget http://ck.kolivas.org/apps/cgminer/antminer/s4/4.6.1-141018/cgminer
mv /usr/bin/cgminer /usr/bin/cgminer.bak
chmod +x cgminer
mv cgminer /usr/bin/cgminer
/etc/init.d/cgminer.sh restart
I think that might not keep across a power cycle though.
Would ckolivas latest cgminer for the S4 be better then "initramfs.bin.SD-20141016.tar.gz"? Since ckolivas's cgminer is dated 10-18-2014, and bitmains firmware is dated 10-16-2014?