And if you can actually input data using the protocol, you can take some standard packets and tweak a byte/short/long at a time and see what changes.

Reversing USB is the same as any protocol on top of TCP is the same as any other protocol, just with different tools.

I wish there were an open source hex editor like Hex Workshop for Windows - one of the features I loved was tagging a section of bytes with comments, and being able to use those same tags across multiple data dumps.