Fetch upstream and apply:

git fetch upstream
git branch -va 
git checkout master
git merge upstream/master


Compile the kernel. Full instructions at http://mythopoeic.org/pi-ntp/

export CCPREFIX='/usr/bin/arm-linux-gnueabi-'
make ARCH=arm CROSS_COMPILE=${CCPREFIX} oldconfig
(optional) make ARCH=arm CROSS_COMPILE=${CCPREFIX} menuconfig

make ARCH=arm CROSS_COMPILE=${CCPREFIX} -j5
make ARCH=arm CROSS_COMPILE=${CCPREFIX} INSTALL_MOD_PATH=/home/user/raspberrypi/ntp_mods/temp_modules modules_install

clone the firmware repo: https://github.com/raspberrypi/firmware.git


Copy the following:
The kernel itself: from linux/arch/arm/boot/zImage to /boot/kernel.img
The modules directory: from /home/user/raspberrypi/ntp_mods/temp_modules/lib/modules/3.12.21+ to /lib/modules/3.12.21+
The kernel firmware directory: from /home/user/raspberrypi/ntp_mods/temp_modules/lib/firmware to /lib/firmware . Note that if you have any custom firmware (such as for a wireless network adapter), you'll need to copy it back into the new /lib/firmware directory.
Bootloader-related files (from above git repo):
firmware-next/boot/bootcode.bin to /boot/bootcode.bin
firmware-next/boot/fixup.dat to /boot/fixup.dat
firmware-next/boot/start.elf to /boot/start.elf
GPU-related files: from firmware-next/hardfp/opt/vc to /opt/vc