[Nexus 7 Android Development] Juzman:
I completely removed System Tuner. I have 1 script in init.d (90system_tweaks). I know (part) of it works. The remount, the fsync and zRam stuff. Also the CPU undervolting, it's just the max_frequency doesn't stick.

#!/system/bin/sh
#--------------------------
# Nexus 7 Tweaks
#--------------------------

#--------------------------
# remount /data for faster i/o
#--------------------------
mount -o remount,discard,noauto_da_alloc /data /data
mount -o remount,discard,noauto_da_alloc /cache /cache

#--------------------------
# disable fsync
#--------------------------
echo 0 > /sys/class/misc/fsynccontrol/fsync_enabled

#--------------------------
#set zRAM size (recommended sizes are 64 and 128)
#--------------------------
echo $((1024*1024*64)) > /sys/block/zram0/disksize
/system/xbin/busybox mkswap /dev/block/zram0
/system/xbin/busybox swapon /dev/block/zram0

#--------------------------
# modify cache
#--------------------------
chmod 777 /sys/block/mmcblk0/queue/read_ahead_kb
echo "1024" > /sys/block/mmcblk0/queue/read_ahead_kb
chmod 777 /sys/devices/virtual/bdi/179:0/read_ahead_kb
echo "1024" > /sys/devices/virtual/bdi/179:0/read_ahead_kb
if [ ! -e /sys/block/mmcblk0/queue/read_ahead_kb]
then
sleep 60
fi
chmod 777 /sys/block/mmcblk0/queue/read_ahead_kb
echo "1024" > /sys/block/mmcblk0/queue/read_ahead_kb
chmod 777 /sys/devices/virtual/bdi/179:0/read_ahead_kb
echo "1024" > /sys/devices/virtual/bdi/179:0/read_ahead_kb

#--------------------------
# modify i/o scheduler
#--------------------------
chmod 777 /sys/block/mmcblk0/queue/scheduler
echo "deadline" > /sys/block/mmcblk0/queue/scheduler
if [ ! -e /sys/block/mmcblk0/queue/scheduler]
then
sleep 60
fi
chmod 777 /sys/block/mmcblk0/queue/scheduler
echo "deadline" > /sys/block/mmcblk0/queue/scheduler

#--------------------------
# change CPU and governor
#--------------------------
if [ -e /data/local/cpu_protection ] ; then
echo failed > /data/local/cpu_failed
chmod 777 /data/local/cpu_failed
exit
fi

echo applied > /data/local/cpu_protection
chmod 777 /data/local/cpu_protection
chmod 666 /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor
echo "interactive" > /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor
chmod 666 /sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq
echo "1000000" > /sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq
chmod 666 /sys/devices/system/cpu/cpu0/cpufreq/scaling_min_freq
echo "100000" > /sys/devices/system/cpu/cpu0/cpufreq/scaling_min_freq

chmod 666 /sys/devices/system/cpu/cpu1/cpufreq/scaling_governor
echo "interactive" > /sys/devices/system/cpu/cpu1/cpufreq/scaling_governor
chmod 666 /sys/devices/system/cpu/cpu1/cpufreq/scaling_max_freq
echo "1000000" > /sys/devices/system/cpu/cpu1/cpufreq/scaling_max_freq
chmod 666 /sys/devices/system/cpu/cpu1/cpufreq/scaling_min_freq
echo "100000" > /sys/devices/system/cpu/cpu1/cpufreq/scaling_min_freq

chmod 666 /sys/devices/system/cpu/cpu2/cpufreq/scaling_governor
echo "interactive" > /sys/devices/system/cpu/cpu2/cpufreq/scaling_governor
chmod 666 /sys/devices/system/cpu/cpu2/cpufreq/scaling_max_freq
echo "1000000" > /sys/devices/system/cpu/cpu2/cpufreq/scaling_max_freq
chmod 666 /sys/devices/system/cpu/cpu2/cpufreq/scaling_min_freq
echo "100000" > /sys/devices/system/cpu/cpu2/cpufreq/scaling_min_freq

chmod 666 /sys/devices/system/cpu/cpu3/cpufreq/scaling_governor
echo "interactive" > /sys/devices/system/cpu/cpu3/cpufreq/scaling_governor
chmod 666 /sys/devices/system/cpu/cpu3/cpufreq/scaling_max_freq
echo "1000000" > /sys/devices/system/cpu/cpu3/cpufreq/scaling_max_freq
chmod 666 /sys/devices/system/cpu/cpu3/cpufreq/scaling_min_freq
echo "100000" > /sys/devices/system/cpu/cpu3/cpufreq/scaling_min_freq

#--------------------------
# CPU undervolt by -100mV
#--------------------------
echo "1137 1112 1100 1075 1050 1025 1000 975 950 925 900 875 812 800 775 750 725 700 " > /sys/devices/system/cpu/cpu0/cpufreq/UV_mV_table

Edit: If I go to Settings -> Performance -> Processor and set that to 1000 Mhz and "set on boot", it works.