I ran into the same problem when upgrading the debian pg package from 7.2 to 7.3. Propably some parameter setting for maximum identifier size was changed on the way. A silly workaround might be to compile 7.3 by hand and set this parameter to the old value, but I'd rather rename to the full names as you did.
Can you share how you dropped and reloaded _all_ the functions - did you find some way to do that automatically? And does everything still work, e.g. views that contain fields computed by such functions?