The new emerge on my system was binded to python2.2 instead of spython. When I unmerged X11, emerge didn't work anymore as python2.2 was linked to X11. This can be helped by setting the *shared* flags in Modules/Setup when building python2.2, this was only a python modules is linked to X11 and emerge will work as normal.
This in an on-going project, and requires a little bit of finesse while executing. Don't worry, though, it's one of my highest priorities!
As of earlier today, things should be in order for a shared Python. I'm closing this bug, but if it doesn't work for you (after rsync'ing, of course), re-open it with some details.