I don't know what ISPConfig Migration Tool does. I am familiar with ISPConfig and use it myself, but found it to be a little bit unstable.
If you have a backup of "data" directory (or the entire "epesi" dir) and the database dump then you will be fine.
Error 503 is a general server error and you need to inspect PHP error log file for details.
Please follow these steps: https://forum.epesibim.com/d/2320-been-hacked-help/4