Per request I'm going to try to expand on this a little bit. I'll write up the instructions assuming you're using adb. There's likely a lot of different ways this can be done, but this is my way. Have adb installed and set up, there's plenty of guides out there on how to get this going. Assume every section starts from a new windows command line. Here goes:
Setting permissions in root explorer:
Hold down on File in root explorer with r/w enabled on /system. Click permissions. Set them. Everyone should have read access, owner should have write access, no one should have execute.
Delete the existing Nfc.apk, Nfc.odex NfcTest.apk and NfcTest.odex files from /system/app.
adb shell
>su
>mount -o rw,remount /system/app
>rm /system/app/Nfc.apk
>rm /system/app/Nfc.odex
>rm /system/app/NfcTest.apk
>rm /system/app/NfcTest.odex
Push the apk's from my zip file's "app" folder to /system/app and fix permissions using root explorer
adb push Nfc.apk /sdcard/
adb push NfcTest.apk /sdcard/
adb push wallet.apk /sdcard/
adb shell
>su
>mount -o rw,remount /system
>cp /sdcard/Nfc.apk /system/app/
>cp /sdcard/NfcTest.apk /system/app/
>cp /sdcard/wallet.apk /system/app/
Open Root Explorer and fix permissions
Push the files from the "lib" folder to /system/lib and /system/lib/hw respectively and fix permissions using root explorer
adb push libnfc.so /sdcard/
adb push libnfc_jni.so /sdcard/
adb push libnfc_ndef.so /sdcard/
adb push nfc.smdk4x12.so /sdcard/
adb shell
>su
>mount -o rw,remount /system
>cp /sdcard/libnfc.so /system/lib/
>cp /sdcard/libnfc_jni.so /system/lib/
>cp /sdcard/libnfc_ndef.so /system/lib/
>cp /sdcard/nfc.smdk4x12.so /system/lib/hw/
Open Root Explorer and fix permissions
Push the file from etc folder to /system/etc and fix permissions using root explorer
adb push nfcee_access.xml /sdcard/
adb shell
>su
>mount -o rw,remount /system
>cp /sdcard/nfcee_access.xml /system/etc/
Open Root Explorer and fix permissions
Make a backup of your build.prop file and push my build.prop file to /system and fix permissions (or you will boot loop)
adb push build.prop /sdcard/
adb shell
>su
>mount -o rw,remount /system
>cp /system/build.prop /system.prop.bak
>cp /sdcard/build.prop /system/
Open Root Explorer and fix permissions
Reboot phone
Set up google wallet and add cards
Restore your original build.prop after everything is set up
adb shell
>su
>mount -o rw,remount /system
>rm /system/build.prop
>mv /system/build.prop.bak /system/build.prop
PROFIT!!