I think that one of the better approaches might be to just graft in a modern SBC (say, something like a gumstix, but with host USB onboard), and link it to the existing logic on the local bus (the same data/control lines that are used for USB, ethernet, and IDE in the current board). Then use it as a modern I/O controller for the existing design.

The mass storage could be left to the existing logic, or taken over by the new SBC, which would solve the speed issues. It could reexport the storage to the empeg board over an emulated storage adapter (simple, custom driver), or even over NFS/FTPfs via ethernet.

Mmm..