Looking through System Failure, The Yamatetsu MetaMatrix, UOL, PacRim Comm, Angel Sat, Arespace, Shiawase, MCT and Wuxing were the first to be hit with worms. There was also a worm at Europort, one on the Singapore MRG, and Puck's worm that hit Deus at Boston. Eleven worms total that have been detailed.
There were 15 EMP bombs set up over major cities, set to go off when the virus killed the LTG. Unfortunately, this doesn't mean there were code eggs at each location, but we might be able to assume so. So, I'd put a very rough estimate at between 15-25 code eggs.