Tex24

So I recently bought a 2012 with an SCT tune on it and it was set for 93 performance. After I fill up it does this really rough shutter for the next 5 minutes on and off every 5 seconds. Well now it does that rough idle just not as violent as when you first fill up and I don't know if its a ****ty tune or what. Also when I depress the clutch there isn't any noise but when I let it go in neutral it makes a really loud rattling sound coming from the trans and during these on off cycles of the rough idle it goes quiet then picks back up. sounds to me like the tune or maybe heads cause I haven't driven another V6 S197 but it almost feels "raspy" if that makes sense and I can feel a decent amount of vibration through the pedals and the shifter. anyone have any of these issues before who can steer me in the right direction. Thanks in advance.