Axle parts and pieces

You do not remove the pinion shaft, you remove that big nut and pull off the yoke (the part your U-joint attaches to). If there is gear oil in it and it is not leaking, leave it the hell alone. Playing with it is not in the realm of "preventative maintenance", only "convenience if yours is bad"
If you do it anyhow, the gears are not affected by removing the yoke.
Second question... NO
There are no bearings that require attention in your axle. They are all five lubricated by the gear oil that is in the pumpkin. All you should do is lay one side of the axle down hill for ten minutes to let the oil run down, then do the same for the other side before bolting it up. You can not access the bearings without pulling the shafts and the pinion. Again, if something wasn't right (binding, squeaking, rattling, lots of rust dust) you should attend to it now, rather than later. If everything looks good, then leave it alone. You should be able to freely (it is heavy) move the axle shafts back and forth. Likewise on the pinion yoke. If it all rotates without squeaking or grinding to a halt, then rest assured. All is well.
Your axle came out of an 87, not an 88. It was not offered that year.
Sealed bearing is the wrong name. They are regular caged bearings all around. You can hand pack them with grease, but not without pulling everything apart to do it. Then, the grease would expel itself in ten minutes on the road and be replaced by the gear oil that is supposed to be there. All of them will be wasted by removing them, so don't try. They will either need to be pressed back on, or you runthe risk of wallowing out the holes if you do it with a hammer. The races that are in the axletubes will be stuck as well. Don't try it unless there is a problem.
You can and should double check the parking brakes, the caliper pads, and that you have the right fittings to attach it to your Jeep. I used stock Cherokee front hoses to add a flexible end to the caliper (makes it easier to service it if you are not bending lines to remove the calipers - see pictures) You could do that. Maybe you could change the diff fluid, pull the cover and clean it all out with brake cleaner, that could be good as well. Then use RTV to reinstall the cover. It is easier and cheaper than the real cover gaskets.
Other than that, you should just stick it under there and go for a drive. If you have a good set of tall jack stands (under the frame raising both back tires off the ground) and an angle grinder for the u-bolts, just do it. You would have it done by now for all of the e-mailing you have written me.
Cut the old one off, pulling drive shafts and brake lines before. Then lower it balanced on your floor jack. Put the new one up on the floor jack and raise it into place. Attach using the u-bolts, torque appropriately, cut off the excess thread, and bleed your brakes. Insert driveshaft and crack beer. it is really that easy.
Now get to it. for me, two hours, for you, budget four. It still can easily be accomplished in a free evening if the weather is good. Offer free beer and pizza to friends who show up.
-bc