I am have replaced thermostat, water pumps seems good, 3 core radiator, had electric fan hooked up constant, add additional electric fan, only over heats with elevation change, from 3000 to 6500 square feet, does not over at high or low elevation only when driving up the incline.

At what temp should the car overheat and boil over?

The elevation thing has me confused, my 00' XJ has been all over, never noticed a problem relating to that, however I would look at your water pump, it may "look" ok, but it could still be the problem. Unless your pulling something, all those fans aren't needed, especially with a 3 core rad. Not sure if your XJ has one but check your MAP sensor, that senses air changes(elevation). Also look at your fan clutch, it may not be working properly.

Oh, also if you haven't done it yet I would recommend giving your coolant system a good flushing, you could have some crud in the engine coolant jackets causing your problem.

THe truck is probably overheating not because of elevation pressure changes but because of the stress of climbing the elevation. A few thoughts come to mind. First, are you sure you got all the air out of the system? Second, although the rad may look good, it may be clogged. Third, do you have a fan clutch along with two electric fans? The fan clutch is a big factor. If it isn't working right, it can cause you to overheat. Also, if you do have elec fans too, are the set up to pull air or push air? The fans may be counteracting each other. If you are not sure, take a piece of paper and with the motor and fan clutch running place the paper in front of the rad. If it gets sucked to the rad, it is pulling, if not it is pushing. Next turn on the elec fan. And see what happens there. They should all be doing the same thing. Hope this helps.

What kind of thermostat did you use? The after market units don't have the small hole in the top. This will cause your over heat problems. Go to the dealer and get the correct one and install it with the hole at the top. My 90 cherokee had the same problem and when I removed the old thermostat it was an aftermarket unit. I purchased the correct one from the dealer and installed it. The jeep runs at 210 degrees. Which is normal. If you have the closed cooling system you can change it out to an open system for about $240.00. The open system is far better and you'll have less problems in the long run.