I made a new modifications to cgminer.sh to make the clock configuration easier to adapt and save between reboots.

The modification will read the clock settings from the file /config/clocks.conf and apply them when cg/bfgminer is started.
The syntax of the config file should be self explanatory.

Add in the beginning (where the other similar lines are) to cgminer.sh :

CLOCKS=/config/clocks.conf

And a bit further down:

if [ -n "$good_ports" ] ; then
if [ -f $CLOCKS ] ; then
clocks=$(cat $CLOCKS)
else
clocks="0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 0x02,0x01 "
fi

di=0
for p in $good_ports ; do
# Re-enable PLL
i2cset -y 2 0x71 1 $((p+1))
for c in 0 1 2 3 ; do
cmd=$(printf "0x84,0x%02X,0,0" $c)
spi-test -s 50000 -OHC -D /dev/spidev1.0 $cmd >/dev/null
cl=$(echo $clocks $di | awk '{split($0,a," "); print a[a[NF]+1]}')
cmd=$(printf "0x86,0x%02X,%s" $c $cl)
spi-test -s 50000 -OHC -D /dev/spidev1.0 $cmd >/dev/null
cmd=$(printf "0x85,0x%02X,0,0" $c)
spi-test -s 50000 -OHC -D /dev/spidev1.0 $cmd >/dev/null
di=$((di+1))
done

# re-enable all cores
i=0
while [[ $i -lt 192 ]] ; do
i2cset -y 2 0x2$p $i 1
i=$((i+1))
done
spi_ena=$(( spi_ena | (1 << $p) ))
done
fi

Example /config/clocks.conf:

0x02,0x71 0x02,0x71 0x02,0x71 0x02,0x71
0x02,0x71 0x02,0x51 0x02,0x71 0x02,0x51
0x02,0x51 0x02,0x51 0x02,0x51 0x02,0x51
0x02,0x51 0x02,0x51 0x02,0x51 0x02,0x51

Spaces are very important in this file. Do not add a space after "0x02,".

I hope its useful