The one thing it does do is keep asking to open door 2. I have set that door as no door there. Nothing I seem to do stops it from asking to open door 2.
That's entirely normal. You are confusing [exit2] as if it had anything to do with the "Door 2" command.
Any [exit] can be associated to any code. What you did, was to tell GSX this airplane doesn't have two of the up to four passenger exits, but this is entirely unrelated by the code the door is associated. You could have all passenger exits to be associated with code 1, or each one to a different code, it depends how the airplane was made.
The message to open "Door 2" correctly appears, because you set both cargo doors are controlled by the standard FSX variable for the door 2, which on a default airplane is used by cargo doors, that's why GSX defaults to it when you start configuring a new airplane.
So, if the door is open, but GSX is still asking for it, this indicates that door, in this specific airplane, is NOT controlled by the standard FSX variable for cargo doors.
Captain Sim usually have their own custom L: variables, so you should use the option to write a custom XML expression for the door, see the example in the GSX manual, you will only have to replace the L:MyVar with what Captain Sim used for that door for this specific model.
The names of the variables used can be usually found using an hex editor to open the external .MDL file of the airplane.