Whiskey Jack,
With your screen name I'd figure you lived in Lynchburg, TN
Yes, if you change the heater hoses, remove them from the XJ, then at your work bench use a hack saw to cut through the band and then remove the hose. This will allow you to reuse the wye fitting.
I am still running the stock cooling system configuration but three plus years ago I was in the same position as you, do I convert or stay with the stock cooling system. I found out both radiators are idential in size so installation not a problem. Also you use the same P/N radiator hoses since they will hook up the same.
The main problem is where to put the switch to turn on the electric cooling fan. On the stock radiator there is a fitting for it to mount in the cold tank. It that sensor with 1 1/4" hex on it. The later radiator does not have a openting to mount the sensor.
Chrysler came out with a fitting to install in the lower radiator hoses but in 2000 the part was no longer avaiable. So if you read about the part on the web sites it a thing of the past no longer available.
There have been discussions on brands of radiator GDI vs modine, do a search on this, someone posted GDIs new numbers. They were having quality problems and changed the number once they instituted new quality measures.
The part people over look is the heater hoses. I have never seen this written down but to fully convert to the post 91 configuration you should change out the return tube for the water pump. If you did this then using the post 91 heater hoses and valve should be painless.
With 200,000 miles you might want to install a new water pump since it could be a stock unit. With the radiator out with will have lots of room to change it.
There has been talk on here about sources of water pumps, you can get aftermarket high volume pumps, rebuilts or even new ones. Don't over look the dealer for a new water pump.
I do like the mopar water pump and thermostat gaskets. I recommend you use them regardless where you get the water pump; however, as most people on here will tell you use a Mopar 195F thermostat.
If you go to the dealer ask them about the water pump pipe then can fill you in on the differences between the 88 and post 91 versions.
I personally like having a reservoir of coolant above the engine, it assures the engine if full of coolant/no air pockets. Even with that said the plastic pressure bottle is the weak point of the system. There are people who have replaced the plastic pressure tank with the moroso surge tank. Eagle is the one that comes to mind that has done that.
martin