What platform are you compiling for? I just tried compiling the latest from bioperl-live and Build.pm has been removed from Bio/Root. I know that CJ has been making a lot of changes to how the modules are organized. I would jump on the IRC channel to get help by the devs, frankly. Can you do with just the latest release, or do you need a specific patch?

EDIT: Can you just export PERL5LIB=/path/to/bioperl-live:$PERL5LIB?