Maybe your air locked.
I found the best was to fill the radiator on my 87, is to remove the top hose from the thermostat housing and fill the radiator and block that way. I also remove the heater hose from the thermostat housing, its my full gauge. When coolant comes out its full and it also lets the air out.

 

The "R" stamped on the pump means REVERSE.

The new pump should be stamped "R" as well or it is one of the standard rotation pumps.

 

i would say air also if belt was on properly and the replacment WP is same as the original one.

Here are a cpl of links on burping one and drilling the thermostat to self bleed trapped air out.

http://www.lunghd.com/Tech_Articles/...BurpAirMod.htm

http://www.naxja.org/forum/showthread.php?t=86331

 

yea, the old pump has R stamped but the new one does not, yet they are identical.

 

those water pump pics are the same part. If it was reverse rotation the fins would be facing the other direction hence pumping fluid the other way. i dont think the water pump is your problem. You said the over flow filled with clear liquid? thats strange if you put coolent water mix in it how is this possible? probably air lock try filling it like Caish said thats how i did mine after it air locked and it was fine after that. Good luck

 

success!

over the past 2 days my dad and i put in the new timing chain, kept the water pump napa gave me, had some trouble putting the harmonic balancer (really TIGHT fit). ended up having to re-tap the threads in the crank to accept an extra bolt we had laying around (the old one stripped because the HB was so tight). then everything went in fine. put everything back together, filled it up with coolant, started her up and she runs perfectly now! no more sound and no more over heating!


thanks everyone for all your help!

 

Your new water pump is the wrong one it has a R stamped because the Cherokee's need a reverse water pump that is your problem... also after draining fluids there is a very good possibility that there might be an air pocket trapped in your head creating steam not allowing your thermostat to open just drill 2 holes in the thermostat to bump the air hopefully you can figure it out good luck