Update—as of mid-2004, the engines and props have been pulled from the XC-99 and shipped to the USAF Museum in Dayton. Disassembly of the aircraft continues. The USAF Museum has made the XC-99 a priority, but they are still looking for an economical way to move the larger parts of the aircraft.
Update—as of mid-2005, the XC-99 has reportedly been fully moved to Dayton for restoration. The USAF Museum has reportedly found funding to restore the XC-99, and plan to make it the centerpiece of a new display of X-aircraft.
Update—as of mid-2006, I visited Kelly USA, and saw that the main fuselage of the XC-99 is still sitting on the ramp at Kelly. The wings and engines appear to be gone, and those are likely the parts that have been moved to Dayton so far.
Update—as of early 2009, it was confirmed that the XC-99 has now been fully disassembled and was moved to Dayton during 2008.
Update—as of 2011, the XC-99 was taken off of restoration status and tours were no longer allowed to the aircraft. It was later decided to move the XC-99 remains to Davis-Monthan AFB in Tucson for storage in a dryer climate to prevent any further deterioration. The USAF Museum decided to focus on the new 4th hangar that is being built and didn't have staff time or funding to do everything, and the XC-99 restoration was suspended as a result.