We do a lot of migrations from custom systems or SaaS integrations to Kill Bill (open-source subscription billing and payments platform) [0] and we've summarized our strategy and usual pain points in our migration guide [1]. You might find it useful.

Happy to chat offline too if you want to go into specifics.

[0] http://killbill.io/ [1] http://docs.killbill.io/0.16/migration_guide.html