This isn't pretty. And i've probably left out a critical step.
Core concepts: making some changes directly in the database. Enabling head2head and alpha2alpha in the database (setting both status and schema_version). Manually commenting out the update hooks that i did in the database to make user module's updates work so that alpha2alpha's can work.
Setting the line in alpha2alpha.module to give the current version:
<?php
$version = variable_get('alpha2alpha_version', 7);
?>