To be honest you shouldn't blame the machinery for poor owner maintenance. With a loose motor mount the vibrations could have caused many problems with various components under the hood including the water pump. Unfortunately it sounds as if the vibration may have damaged your PCM, their pretty damn fragile (I've replaced two already). I am currently repairing a very similar problem. I had the misfire on injector 4 code as well (still do) and it WAS running very rough. I spliced the signal wire (wire coming from PCM) to injector 5 after performing various troubleshooting. To troubleshoot it, simply unplug the misfiring injector plug, if the engine doesn't bog down, remove injector 5's plug (it will bog down) then plug it into injector 4. If the engine Idle improves, the injector is good. If so, take injector 4's plug and now plug it in injector 5. If no improvement the PCM isn't properly sending signal to the injector. At this point, you have two options. You can try to replace the injector plug (sometimes the go bad) but I would suggest tracing the signal wire to the computer and putting a volt meter from the signal pin on the PCM, and to a ground. Now compare with a working injectors terminal. If different....you have a short/bad PCM. As a temporary fix splice the injector 4 plug signal wire with injector 5's signal wire. (This will make the Jeep run MUCH better but not its best. Also CEL will remain on). This only works in I6 motors since the fire in-line. The timing will be off slightly so she will still run sluggish but much better. To fix the PCM simply go to junkyard and match your PCM's model number with another computer and do a bolt on replacement. Note that 1998 and later models need to be brought to the dealer to be reprogrammed/flashed to suite your vehicle and update VIN# information. Older models do not require this. Good luck, and in the future if something as important as a motor mount is going make sure to replace it right away otherwise you run the risk of damaging other parts. Jeeps are resilient but not invincible.
1997 Jeep Grand Cherokee 4.0L I-6 150,600