Not quite. The trans control unit (TCU) decides the shift points based on the output shaft speed sensor. the throttle position sensors, and input from the NSS shift sensor. It doesn't get anything from the engine computer. It doesn't need the engine computer or VSS in the xfer case. The newer AW4 also has an input speed sensor which is used to diagnose shifting problems. For example if it's commanding 3rd gear but appears to be in 2nd it will throw a code for a bad solenoid, but as far as I know it doesn't do anything different when something like this is detected.
The throttle valve cable is sometimes incorrectly called a kickdown, but as noted it only controls the hydraulic pressure and not the shift points like older non-electronic controlled transmissions. If it's not connected, you won't have enough hydraulic pressure to shift properly. It will either shift very weakly and possibly burn up clutches or just won't move at all. It comes off the drivers side, midway along the side lower down towards the pan. You actually have to remove the pan to disconnect it, so I'm surprised it's missing.
The second cable on the XJ shifter is probably the interlock cable that goes to a solenoid up near the steering wheel that actuates when you have the vehicle turned on and the brake pressed. You can remove and toss it, just beware that without the interlock setup, you'll be able to shift in/out of park without the key in and remove the key with it still in neutral or park.