In that case, it's mainly going to break down to personal preference. Do you enjoy driving an auto or manual more? If you go auto, remember to get an external transmission fluid radiator. All of the Jeep auto transmissions have a bit of a habit of overheating if you ride the torque converter on obstacles or crawl up hill for an extended period of time.
I'm no expert, but Novak implies that you HAVE to have the PCM from an '87 to /01 Jeep 4.0 to control the electronic shift points on the AW4. Make sure you have that wiring harness worked out before you pull the trigger. Either your YJ or the Comanche PCM should work, as long as they don't have different plugs.
The Jeep AW4 Transmissions - Novak Conversions