DevShop or AegirUp may provide a quick way to get your site into Aegir if you want to leverage those benefits.
If not, consider leveraging Drush to help. Aquia posted a guide for for that: https://www.acquia.com/blog/use-drush-upgrade-drupal-6-drupal-7
I also found it helps to vet custom projects with the coder module before hand. If the projects pass the coder tests in D6 then run the upgrade tests for D6 -> D7.