How long ago did you do the water pump? Sometimes the coolant in the overflow will go down as the air is being self-bled over time but will eventually stop. Any major bubbling from the radiator when running w/the cap off?
'05 WK Limited QDII, Superlift 6", Bilstein struts,315/70/17 Duratracs, Gibson CB, Volant CAI, JBA UCA's, JKS quick disco, adj. Rear trac bar, 4xguard armor, Diablosport Intune, Xenondepot 6000k HID's, Putco Jet yellow fogs.