Upgrade process as currently understood:
https://etherpad.wikimedia.org/p/Civi_4.6_staging_deployment
Beat on our custom modules and the integration between subsystems.
Prioritize work by whatever causes unrecoverable data loss sort of situations. If we can fix it later, don't sweat.
Emergency protocol
Note that rolling back an upgrade would be a big effing deal, so test thoroughly and realistically. Iterate generously.
Consider installing an audit mechanism before the upgrade (T115731), so that manual entry is not lost in case of rollback. This would give us the ability to replay some of the lost changes, or at least see them listed.