Sounds like a blown HG with the milkshake. Suprised on such a low milage 4.0L. Engine compression test and/or cooling system pressure test should show where the leak is.

The rusty water in the rad makes me wonder if your radiator is bad. My 91 XJ had the rusty brown water problem for a long time and finally resulted in a bad overheat one day. Replaced the rad,water pump and thermostat and things have been fine with it for a few years now. The anti collapse spring inside the lower rad hose rusts out pretty easily, mine was rusted into pieces and probobly contributed to plugging the radiator.

Took about an hour to chemically flush all the brown nasty water out of the block and cooling system.
Runs alot cooler too,below 200 instead of over 210.
Good luck, hope it's just a rad or gasket and not anything major.