This seems a bit odd. 4.0.1 seems to be a bugfix releasej rather than a improvement release, otherwise I would expect a 4.1 revision. I purchased my YDL4 disks some time ago, and some things (like MOL with OS9) have never worked on my G4 system.
In any case, most of the updated packages seem to already be in the "public" yum repo, minus the kernel.