I have somehow scratched the rod for the manual trans in my 2012 a bit while whacking off the knob, cars only done a couple thousand Ks so wondering how difficult / costly it is to find this part and replace. If it's not too expensive ill switch in a new one, otherwise what would be best to touch up this with?

 

You will have to get a doner rod from another JK, pull your center console out, there is a bolt that holds the rod in. See if yours is the same and make the switcheroo.