Your USB drive is configured in the new way, so you don't actually need these tools as your PC will just read the data.
What you do however need is
God2ISO to convert the installed game (GoD) to an ISO, this would be the Data0000 files you have.
You can then use
Xbox 360 XISO Extract to extract the ISO you made and see the files / folders that would have been on the disc.
It's a bit of a process, however the only way I know of to obtain data from a non modified Xbox 360 DVD.