To clone one empeg onto another, the easiest way (for me) is to have a third machine running Linux, with mirrordir software installed.
First, use the serial port to login to the target empeg ("empeg2") and issue the "rw" command (yes, I know.. I'm working on making this easier..).
Then, from the Linux box on the network:
mirrordir -v
ftp://empeg1/ ftp://empeg2
Come back a few hours later, and you'll have two completely identical empegs, except for kernels and other stuff stored in the flash.
Of course, there's a bug I just found in kftpd that causes mirrordir to have trouble every 64 files or so.. that will be fixed shortly in Hijack v121
-ml