I posted a 001 mod on the TapeOp board a couple months ago which upgrades channel 1 and 2 preamp IC's:
http://messageboard.tapeop.com/viewtopic.php?t=39322
It has nothing to do with the clock, converters, or software. Just the 2 channels.
EDIT- btw, people have asked if I wanted to do the mod to their 001's and to be honest, no. It can be done in an hour or so by any good tech with surface mount experience.