There is the ongoing Boeing CPCP programme which seems to deal with most concerns. Alongside that there is a fairly constant stream of service bulletins continuing to deal with keeping these older birds safe.
The latest we received a couple of days ago being SB 747-53A2431 R02 dated 13th June deals with problems found in high time aircraft relating to cracks and corrosion in upper deck floor beams at STA 340, 360 and 380 that might in some circumstances effect fuselage integrity. They also refer to Boeing Structural Item Integrity Advisory (SIIA) 747-175.
The aircraft refered to above was a 747-200 Freighter with 19,598 flight cycles and 79,975 flight hours. The problem was identified, rectified and the service bulletin issued accordingly.