How do you debug problems with a migration?
Logs should be written to craft/storage/runtime/logs to help debug issues like this.  It gets a little sketchy with fatal errors, though.  Logs get flushed to disk when the onEndRequest event gets successfully fired.  If it's a fatal error that kills script execution, that event will never get fired and the logs don't get flushed.  That might have been what you're running into here.

Outside of that, to answer your original question, the absolute best way to debug stuff like this is with xDebug.  PhpStorm has a native xDebug client built in and it's pretty fantastic.