Great work by everybody so far, especially Paul! Very inspirational.
Looking at the schematics, it looks like the unused IO pins on the microcontroller don't go anywhere. If that is true, would it be possible to have those unused pins going to a pad? I think that would make it easier for people to extend the controller in the future by adding their own features (the beauty of open source!). One idea I had for an extension was an anti-theft feature. Maybe different features could be enabled by jumpering some of the unused pins high, which the end user could easily do if the pins were available on the controller board.
On the topic of USB devices to replace your hobbled oscilloscope, check out this DAQ:
NI USB-6008 - Products and Services - National Instruments
I could probably get a discount (~10%) on it if you are interested.