Just solder protection paint coming off - as long as the tracks stay in place there's not much to worry about. Covering the exposed spots with a piece of tape won't hurt though.
If any tracks got lifted off the PCB you'll need to fix them down and ensure that there can be no short. The quick-and-dirty method is using hot glue.
As to the shielding: you'll need to remove all of the port screws in order to take out the board (usually they are not identical). Be careful when putting them back - they're easily overtightened!
In general: I would've used a piece of cardboard to cover the PCB before putting tape over it. That way you can avoid issues like this.
