adb cmd not working, is my phone rooted? I don't get it.

I want to deodex my phone. It isn't happening and people have said the reason is the phone isn't properly rooted. What gives?

Flashed stock ROM with Odin

Model: S4 Mini i95195
Android Version: 4.2.2.
Baseband: i9195UBUBNE2

Guides I followed:
How to root Samsung Galaxy S4 mini
How to install CWM
How to deodex a Samsung Galaxy S4 mini

I have a RootChecker app that certified that before I installed the RootKit2 package listed on XDA, the phone was not rooted. It indicates it's rooted now.

That last one (deodexing) is where the problem arises. Setting my Windows Path: ;C:\android.sdk\platform-tools, I get the following output in the cmd when I try to initiate the adb functions:

C:\android.sdk\platform-tools>adb shell
shell@android:/ $ su
1|shell@android:/ $ stop
shell@android:/ $ mount -o rw,remount /system/ /system/
mount: Permission denied
255|shell@android:/ $

From what I have been told, if the phone was really rooted it would list "#" instead of "$", which it doesn't. So I don't understand what the problem is.