Proper power design for a USB device
You are correct about the floating nature of the wall wart output.
There's no harm in leaving USB +5V unconnected.  On the other hand, you might have to connect it to your controller, because that's part of its scheme for detecting the USB connection.
Connecting USB GND is necessary.  D- &amp; D+ carry a differential signal, however the common mode needs to be within the operational range.
Self-powered USB by itself doesn't required galvanic isolation.  Whether or not your instrument requires galvanic isolation (and where to have it) depends on the application (?) of your instrument.


A sketch of a self-powered USB device can be found here see 6.2 on p.24.