For the differential, I'd stick with a good mineral-based (non synthetic) gear lube like Valvoline 75W-90. Some very well respected axle manufacturers like Currie have found that gears run hotter with synthetic gear lubes so they require a non-synthetic gear lube to keep the warranty in effect. After much research, they found that synthetic gear lube doesn't "sink" (pull) the heat away from the gears as well which is why synthetic-filled differentials are cooler, but the gears themselves are hotter than with a conventional mineral-based gear lube.
For the MT-90 tranny gear lube, you'll need four quarts as your transmission holds right at 3.3 quarts.
For the transfer case, any good quality ATF is fine. I'd use any good quality brand like Valvoline, Mobil, Pennzoil, etc. No need to spend more for something expensive like ATF+4.
Ignition wire-wise, the very best you can do is to get a set from the dealer. They're very high quality and don't cause radio noise like most aftermarket wire sets do. If you can't resist running aftermarket wires, avoid any that push "low resistance" which does not (contrary to what seems to make sense) give a "hotter" spark. The low resistance type plug wires (even if they say something like "RFI (radio frequency interference) Suppressed) will instead create extra noise which your radio/audio system will pick up.
That '98 you bought will not be fussy about spark plugs as the newer TJs are. Yours will run fine on nearly anything but resist the gimmick plugs like Bosch Plus2 or Plus4 (our TJ engines don't run well on those particular plugs), or Splitfire. A good standard plug is the Champion #4412 Truck Plug. What I prefer due to its extremely long life and good performance is the Autolite AP985 plug which is a platinum. I got over 90K miles out of my last set and they were still at the .035 original gap when I pulled them. Don't let the auto parts store guy talk you into a more costly plug with platinum on both sides of the gap like an Autolite APP985 (two P's in the p/n) as it just costs more with no performance benefit in your particular engine.
Scratched soft top windows are best polished with a multi-step polish like is made by Novus or Maguires. Both work well to remove scratches that aren't too deep but they do take some real elbow grease to use. To avoid scratching them, never ever (!!!) use paper towels on your plastic windows. Paper towels are made from wood products which will eventually turn a plastic window opaque. Instead, use a slightly moistened soft cotton terrycloth towel.
That'll get you going, good luck with your new Jeep.