Set your multimeter to continuity mode and test the traces from the usb port ground, vcc, tx, and rx pins and see if they all connect to the mc. If they don't than that's the first place to start troubleshooting those traces.
If that's all good, try making sure that all the surrounding components for the MC are working. i.e. the clock, and surrounding resistors/caps and whatever else is on that board. The keyboard matrix itself won't stop the MC from connecting and showing on your computer, so we can troubleshoot that later on. As you say, the keyboard is now showing up on the computer, which I think means that it should be fine and recoverable.
The next step would be to try reflash it using the guide from winkeyless, and definitely jump those pins with the paper clip as that will put it in debugging mode