Yep, if you shorten the data ports you cannot use the usb port anymore.

In the meantime I kinda "solved" that issue by using a tiny dip-switch. With that switch I can, at least manually, shorten and "un-shorten" the data ports.
I placed the dip switch in a place where I can access it, at least somewhat, from the outside. When looking at the N9 from the front, I placed it in the upper right edge and access it through the top undeneath the rounded part of the cover of the sim card holder. Of course, in order to actually use the switch I then have to remove the sim card holder, which is actually not a quick way to switch between the two states but at least I don't have to open the case anymore.
As a nice side effect, this solution does not ruin the nice look of the N9.

With respect to actually loading via the touch stone. I discovered that the touch stone thing is really, really picky about being correctly placed. We are talking about millimeters here.
Also note that loading via touchstone is significantly slower than loading via USB.
Additionally, I'd recommend to not load via touchstone unattended. Just in case something goes wrong. You have to keep in mind that this is quite a "brutal" hack.
Right now, I am back to using the USB port for charging. But this is also because I experimented quite a bit with nemo and dual booting and thus need to have data connection via USB. Furthermore, keep in mind that the touchstone is usually placed at a more or less fixed position. In my daily work flow, I use to charge at many random places right now, so I wouldn't use the touchstone that often anyhow.

In any case, please be sure you know what you are doing. This is pretty much uncharted territory and you do this all on your own responsibility and risk.