There is a flange tool to hold the flange while you remove the nut on the yoke, but most guys just use an impact gun. Even one of the 18v or 20v dewalt cordless guns might do the trick. If you only have hand tools, then the right size socket on a powerbar should do the trick once you raise the jeep high enough to get some room for movement. Lock up the parkbrake and have the Jeep in first gear and 4 wheel drive to help hold the shaft from turning.
You do not have to mark the shaft/yoke for relationship. They are not timed.
Buy a seal puller from Princess auto. They are a copy of the snap on and OTC pullers.
https://www.princessauto.com/en/deta...er/A-p2990539e
Pack a little grease on the inside of the new seal so you don't knock off the spring when you are hammering the new one in. Also, run a smear of RTV silicone on the outside edge of the seal before you drive it in.
While you shouldn't hammer directly onto the seal, you likely will have to hit the edges to get it to start. A suitable size pipe or socket which pushes close to the outer edges of the seal can be hit with a hammer to drive the seal in to where it belongs. If you deform the outer face of the seal, then it will most likely leak.
Some spicer yokes have a little rubber washer in the shape of the splines which compresses between the yoke nut and the shaft. Smear RTV in the washer under the yoke nut so the washer seals up the center of the yoke, otherwise oil will travel down the splines and leak out the center of the yoke.
There likely is a torque spec for the nut but since this location does not have a compressible sleeve for the bearings the way a differential might, just tighten it to goodandtight. If you really want the torque spec, google is your friend.