Given that you're backing into Native mode from SharePoint Integrated mode, I only see one possible way through this:
- Setting up new Native RS Server
- Migrating each report one at a time, as no tools I know of exist to automate this kind of migration, this URL might be helpful too: https://msdn.microsoft.com/en-us/library/hh759331.aspx
You may be able to automate some of this, extracting reports from libraries and putting in Reporting Services via PowerShell, if you're up to it start building some custom scripts.
A lot of these reports may tie into data sources in SharePoint and would require some inspection before outright migration as they may not work on the other end.