when you flash this, the CSC gets blanked which kills the S-Pen features
you need to reflash the CSC files from here: http://forum.xda-developers.com/showpost.php?p=62575684&postcount=42
using ODIN, select AP etc, takes 30 secs.
When you say kills the s-pen features..what do you mean exactly as mine is working fine...

I've only ever had stock on my Note 4 so I'm not sure how.