
well good news

At this point in my wrenching life Im thrilled to be able to help out. Pretty frustrating doing this over the net and not being able to get hands on I must admit.
Cooling...Its not uncommon to got lots of air trapped in the cooling system if its just been filled. This will cause some weird problems. The other things that are pretty easy to over look is installing a thermostat backwards. The copper pellet lookin end goes into the head or down into the manifold if its a V type engine.
Unfortunately there is one more that the PO of mine ran into when he replaced the water pump before I picked up my CJ. I cant recall what year your is and when they went to a serpintine belt in the CJ but apparently both water pumps look the with the exception of the impeller. One is meant to rotate CW and the other CCW. He told me the AP store guy screwed up on the pump he bought and he was going nuts trying to figure out why it kept heating up.
If you end up pulling the pump to look pay attention to the way it will spin on the motor. Look at the impeller and you'll see the blades of the impeller will be tilted from the center. Essentially the impeller needs to throw the coolant away from the center which pushed it away and thru the system. If its the wrong one it will look more like its scooping the water and directing it to the center of the pump shaft.
Were all pulling for you to get that first run around the block so keep us posted.