Steve,
If you haven’t noticed it, you should check the OpenSprinkler Pi project: http://pi.opensprinkler.com. This may be what you are looking for.
Regarding your questions:
– The flash is mainly consumed by program code, scheduling algorithms, and a small amount of the Javascript code for serving webpages. The bulk of the Javascript has been moved to external files stored on rayshobby.net server (otherwise there is no way to fit everything in 32KB of flash memory space). The EEPROM is mainly consumed by program settings, program data, and controller settings.
– Server related functions are all in server.pde (pde is the Arduino extension, it is really a cpp file)