For dropping the oil pan you'll need a 3/8s socket set with some extensions. You may have to take the starter off if its in the way, if so unhook the battery. For putting it back on you'll need a new oil pan gasket and RTV sealant, I like the brand "The right stuff", its more money but worth it. You'll also use it later for the diff covers. You'll need a good scrapper to get gasket material off. You'll want everthing nice and clean before putting it back together. May as well get 4-6 cans of brake clean and a few rolls of shop towel. I like the blue ones. Canadian tire is probably your best/cheapest bet for all this stuff. If you have a cordless drill already then get a wire wheel for it. Makes cleaning the gasket stuff off a bit quicker. While at CT see if they have a Haynes manual for your Jeep, it will have nice pics and step by step instructions.
Diffs are easy, put a pan under the center diff, undo the ring of bolts, leave the top one in halfway and smack the cover with a hammer till the seal breaks loose and all the oil comes out. Clean inside with brake clean, clean off old sealer from cover and mating surface. Wipe out the little pool in the bottom of the diff till its empty. Put a ring of sealer on the cover and reinstall cover. Refill with oil, usually 1.5-3L per diff. What kind of locker or limited slip do you have? Some require an additive for the oil.
Manual tranny and t-case will have a drain plug on the bottom and a fill plug on the side. May need a transfer pump to fill it or a long hose to reach up into the engine bay. May need to drain and refill a few times to get it all clear. These may require special sockets, not sure on your model tranny. T-case I usually use large adjustable wrench. This works as long as no one put the plugs in too tight.
Check your owners manual as to what specific oils you need. May need synthetic gear oil for the tranny and diffs($$$$).
It make be worth it to buy a 20L bucket of gear oil(expensive though) and a bucket pump. Will make things much easier/faster.
I wouldn't do an engine flush till the pan has been cleaned out, in fact I wouldn't bother at all. Not really a believer in engine flushes.
No need to pull the valve cover. You won't see mud up there.