Has Alan ever posted his "jackhammer" script for some experts to look at?
I get by really well with a small script that reads the eix outputs, finds the "[U]"
tagged packages, and then runs "emerge -u1" on that list.
Doing anything more than that will be a cause of pain and suffering.
If a package needs patches for something special, it is better to make a local
repository with modified ebuilds and distfiles, rather than try to force the gentoo repo
into your own mess. I do this for a few tthings that Gentoo doesn't ship. Portage
is actuallly quite flexible underneath, itt just takes a bit of learning.