When I changed my Waterpump I did a lot of other stuff while I had it apart. With the age and miles on your XJ I'd consider replacing the radaitor while you are at it, especially if it is the factory radiator With the radiator removed you will have plenty of room to work.
I'd change the radiator, water pump, and thermostat. While changing those I'd insall new radiator hoses, heater hoses, radiator cap, fan clutch, fan belt, idle pullies.
I used dealer gaskets for the water pump, and thermostat. I used dealer hoses for the radiator and heater hoses. I used a dealer radiator cap but I have the closed system on my 88 XJ, you have the open but while you are at the dealer getting the other stuff get a radiator cap it can't be that much.
I had a GDI 3-row for 4 years, but now have a Modine 2-row radiator. I am more impressed with the Modine. I use Distilled water along with the coolant. A guy I use to work at a Nuclear Power plant told me to use distilled water in my car, for the 80 cents/gallon you can't go wrong. It avoids deposits on your new components so the heat exchange process works well.
When you do decide to do this job, make sure you loosen the 4 bolts on the water pump pulley before you remove the fan belt.
While you have the fan belt off turn all your pullies to see if anything is rough, I'd change all the idle pullies as preventive maintenance. I also ended up changing the bearing for the mechanical fan. To chage that you have to buy the AC bracket from the dealer to get the new bearing, you have to buy the next higher assembly, not just the part you want.
If your XJ uses the power steering pump to tension the belt then go to NAPA and buy the Kriket II belt tension tool and use that to install the NEW fan belt you will be installing. I have been using Goodyear belts, I like how they run more quiet than other belts.
I will disagree with people on applying "stuff" to the gaskets. The Dealer gaskets come with RTV silicone on one side. I installed them and have had no problem. I have heard applying sealant to both sides of a gasket actually allows it to float and it never makes contact with the two mating components. I recommend you install as they come out of the box, I did and have no regrets.
Also with the dealer water pump gasket they give you the torque specs. So you will need a torque wrench able to do 10-20 ft lbs. I think using the right torque is most important. So go out to sears and buy a torque wrench if you don't have one... another reason to buy a tool!!!!!!
I think a cooling system renewal is a good thing, once you do it then you won't have to worry for years other than maintain the coolant level.