I second what SJX said to replace. The fan clutch does get over looked and if it over 5 eyars old you have a good chance it is bad. Do not even try to test it, most test give false results, just replace.
If you have a second vehicle remove the mechanical fan and take it to the part store. You can remove the fan so you only have to carry the clutch. Compare your fan clutch to the new one. If they are the same height from where it attaches to the engine to the plane where the fan attaches then get it. There are some aftermarket clutches which are too tall and require you to tilt the radiator to install - avoid those.
Sounds like you may of damaged the thermostat, install a new one and buy it at the dealer.
You may not have all the air out of the engine, here is a good site on how to burp the engine
http://www.olypen.com/craigh/cooling.htm
Also the plastic cooling pressure bottle can be bad or had a bad "radiator cap" on it. You can get a new bottle form quadratec.com for $20, might be worth it. I'd go by your dealer and pick up a cap, I apid $5 a few years ago but they may of gone up.
I think I'd replace the fan clutch, make sure the electric fan is plugged in, pull the temp sensor to make sure the air is out of the block and install a new "radiator" cap on the pressure bottle. See if that fixed the problem, if it does not then take it back to the shop which put in the radiator, there is an implied warranty once they changed the radiator.
I agree on the need for a spring in the lower radiator hose. Did you get new hoses when they installed the radiator? If you have to buy a lower hose get it at the dealer. It very nice, has the spring and anti-chafe installed. I paid $22 if I recall for the lower and $16 for the upper.
But change the fan clutch and radiator cap then if the problem continues take it to the shop. How they react will help you determine if you continue to be a customer. My XJ running hot like describe is a valid reason to take it back.