It's kind of hard to do damage to the transmission if the clutch linkage is not installed. If there is no linkage, assuming that the clutch assembly has been correctly installed, the clutch just won't work. There is a fairly weak spring that holds the pedal all the way up and off the throw out bearing. If there is no linkage to the clutch, and the pedal is not already all the way to the floor, you will be able to push it to the floor with one finger. If the linkage is installed correctly, you should be able to push the pedal about 1" to 1 1/4" easily, (free play), then feel the resistance of the pressure plate the rest of the way. Obviously, the easiest way is to crawl under the Jeep and just look to see if the push rod is between the clutch fork and the bell crank. You need to have this free play. If the clutch pedal is hard to push all the way, that means that the throw out bearing is in constant contact with the pressure plate, and will wear out very quickly. The throw out bearing is only meant to be in contact with the pressure plate during gear shifting, or when standing in gear while running such as at a stop light.