the valve cover gasket is a very common leak and it'll drip down the back of the block and look like an RMS leak. I would check that first.
to gain clearance for the oil pan removal you can jack up the front of the truck so the axle drops out of the way. you'll want all the clearance you can get, but it does eventually fit.
there's a link to a window seal replacement writeup in the link in my sig.
for a 4wheel swap, it's common practice to buy a whole XJ with the drivetrain you want. but this doesn't get you any better gearing.
4.0 + stick = 3.07s
4.0 + auto = 3.55s
and they are the most common out there and are a decent upgrade for a stickshift Jeep with stockish tires.
car-part.com can help with junkyard searches. be sure to search for multiple years, as any AX-15 can work, but the part numbers changed over the years and the website searches strictly by part number. same thing goes for front axles and t-cases and whatnot. first learn what can be made to work, and then go search for what's out there.
rebuilt AX-15s are available out there.
94ish and up will have the external slave.
also, WJ control arms are a good upgrade for a stockish Jeep. they are fully boxed, bent inward for tire clearance while turning, same length as MJ arms, better bushing design, and available new. they just need the metal sleeve inside the bushings trimmed flush with the rubber part.
if you haven't already, read through the "most important tip" thread at the top of this forum.