Despite all of the media buzz about Microsoft partnering with 3D printing companies (including selling Makerbot printers at their stores) & the announcement of 'built-in' or 'native' 3D printing integration in Windows 8.1, performing the upgrade from 8 to 8.1 actually breaks your machine's 3D printing capabilities!
The USB driver acquires the fated yellow exclamation mark, and you'll find your computer feebled in all attempts to connect to any of the Makerbot printers via USB. Attempts to reinstall MakerWare (or just the driver) produce a very vague error.
Fortunately, I found a simple driver signature enforcement workaround is sufficient to get back to printing!
1. Follow these instructions to restart with driver signature enforcement disabled
2. Press Windows+X (or right click on the Windows/Start button) and choose Device Manager. Scroll to where you see the yellow exclamation under USB devices or Ports (it will probably say Replicator). Right click on the device and choose Update Driver. Select "Browse my computer for driver software", then navigate to C:\Program Files (x86)\MakerBot\drivers and click next. Accept the terrifying red warning and your driver will be installed.
3. Happy printing!