Arduino Controlling through C#
Am I missing the point here or wouldn't the C# just have to open a Serial connection to the board and read and write to that to control the program running on the Arduino?
Yes the board is connected by USB, but that's only so it can open a serial connection.
To be honest I don't think you will be able to sample at that speed, you might be better looking at ICs that directly interface with GPIO and RS232/USB.