flat namespace for the config file (its not a real database -- which may be part of the problem

It really depends on how it actually works in practice but it sounds like your end data structure could work better. Depending on all sorts of factors an RDBMS or using a flatfile that stores a hash data structure, serialised with say Storable may help. With the Storable suggestion you would parse the data into a hash (very fast access) then store it into a flatfile with Storable. Anything that needs access just loads the file and gets the whole config hash ready to go. The net result is you effectively spend memory to gain speed.