How did you get on with this process? I think in some cases it might just be cleaner to extract whatever you can from ACS (e.g. device groups and devices, and local identities) and then rebuild the ISE system from scratch. Get a clean perspective and rebuild the logic using the ISE Policy Set. I think a human would do a better job than a migration tool because we can see inefficiencies.
The export/import is useful though - I did a lot of exporting from ACS itself and then massaged the data into the correct .csv to import into ISE. Perhaps the Migration Tool can also do that.