The front driveshafts will have to be changed (the driveshaft for the auto needs to be a smaller diameter) and you'll need to swap rear driveshafts & change their lengths. You'll need to swap PCMs (engine computer), swap your flexplate for his flywheel, and of course the clutch etc.
Personally, I would not do it... you will be losing offroad ability by going to the manual transmission. All the big dogs in competition long-ago switched to automatic transmissions. Even the racer/rock crawler I helped build for the 2008 King of the Hammers desert race (now considered THE toughest event in North America) was set up with an automatic transmission. I converted my TJ from its OE 5-speed manual to an automatic purely for its significant