My 98 TJ 5sp 4.0 had apparenlty leaked 2 qts of transmission fluid into the transfer case... I didn't even know that was possible as I thought a leaking transmission output seal would just leak out the hole in the adaptor between the tranny and tcase. Well, since my tcase was 2 qts over and my tranny 2 qts low I figured that must be what happened... Well, it was time to replace the transmission output shaft seal and the tcase input shaft seal.
Here is how I did it:
Transmission output seal: NAPA 19601
Transfer case seal: Autozone 3173
DRAIN TRANNY AND TCASE FLUIDS FIRST
Step 1: Place jack stand under tranny and put jeep into gear and chock wheels.
Step 2: Unbolt transmission mount (4 bolts centered on skid plate)
Step 3: Unbolt and remove skid plate (6 bolts) and unhook all electrical connectors and breather tube.
Step 4: Unbolt Rear drive shaft from rear diff.
Step 5: Unbolt Front drive shaft from transfer case.
Step 6: Unbolt transfer case from transmission adaptor (6 nuts) and remove transfer case.
Step 7: Remove bolts holding the housing that contains the seal (4 bolts) and clean area thoroughly.
Step 8: Remove seal carefully with seal puller. Clean thoroughly where tcase and transmission adaptor meet and clean old seal area.
Step 9: Replace the seal (I put 3M weather sealant around seal but I doubt this is really needed).
Step 10: Replace the housing that contains the seal onto the tcase with RTV and tighten bolts.
Step 11: Remove seal at transmission output shaft and clean area thoroughly as well as clean the area where the tcase and transmission adaptor meet up.
Step 12: Replace the seal and apply RTV around the edge of adaptor where it meets the transfer case and apply around each threaded studs to create a good seal.
Step 13: Apply grease around the tranny output shaft and tcase input shaft.
Step 14: With the help of friend or transmission jack, jack the transfer case up and carefully align the two and mate them. Tighten up 6 nuts.
Step 15: Re-connect all electrical connections and breather tube.
Step 16: Re-connect both front and rear driveshaft.
Keep in mind this is off the top of my head as I remember it. Be aware of what you are doing and make sure these directions make sense to you before you start. GOOD LUCK!