Ray I think i got it.
Aaron you say you have an overlay on your floor shift selector right? Im assuming you have one like mine where you cant see through it right? If that is the case, YES when you are in D on the console, you are in D on the floor. Same with R, N, P, 1, 2. Now that is a normal car.
You also said you messed with the shifter cable. What and why did you do that?
You also said you cant tell when you put in drive? what about the other gears? Easiest fix I woudl say for that is whatever you did to mess with it, reverse it and dont do it again.