The theory is if you always put your gear shifter into 1 or 14, before you remove the EX box, then if you bump the shifter or stress a cable that can move it before you reassemble, you know where to reset the shifter before you reassemble.
In your case, you say you only have 13 gears. One is missing, either 1 or 14.
If your shifter won't go to 1 on the number plate, the lowest your shifter will go to on the shifter number plate is 2, then you know that when your shifter plate says you are in gear 2 that you really are in your lowest gear which is 1. With the shifter in your lowest gear, remove the EX box, move your shifter to 1 on the number plate, reassemble.
If the EX Box does not want to go on, you have to jiggle your shifter cables a bit so that the hex shaped hole on the cable spool in the EX box lines up with the hex shaped knob on the wheel that your EX box goes over. Just make sure that you did not jiggle the cables so much that you moved the shifter so far that it is no longer in the right gear on the shifter number plate.
Or, if instead your shifter won't go to 14 on the number plate, the highest the shifter will go to on the number plate is 13, then you know that when your shifter plate says you are in gear 13 that you really are in your highest gear which is 14. With the shifter in your highest gear, remove the EX box, move your shifter to 14 on the number plate, reassemble.
I never bother to set my shifter to 1 or 14 before I disassemble because I simply forget to do it. The first time I only had 13 gears on reassembly, it drove me nuts until I realized that I must have bumped the shifter or pulled on a cable which moved the shifter position. Once I figured out how to remedy it, I never worried about it again, it is a simple fix when it happens.
That said, you stated:
...I just removed the gear control box and in doing so realised that one of the cables was jammed up against the bike frame. ...
If one of your cables is not properly threaded through the frame cable guides or has been damaged, that could cause problems that prevent it from working right.
On torque arm issues, I can't comment. I have a Thorn bike which uses an OEM plate instead, not a torque arm.