Replace water pump and heater tube, thermostat, plugs, valve cover gasket (felpro), oil filter adapter, and motor mounts. Clean everything.
Don't forget rear main oil seal. Much easier to do when out of jeep.
My only issue out of the process is I'm now getting a whining noise coming from the tranny when I'm stopped in neutral with the clutch disengaged, once I press the clutch in the noise goes away. I assume its the throw-out bearing but not positive.
TOB only make noise when clutch pedal is pushed down. When foot off clutch TOB not spinning on pressure plate forks. Noise is most likely in trans.