To upload a sketch, just activate the bootloader (press and release the reset-button while holding down the bootloader-activation-button, see the usage guide) and then press the "Upload" button in Arduino.
Frank I did not mean to detract from your achievement.
If you use the Arduino IDE then you can't use V-USB though, I'm going to see about writing a core that works with V-USB. The problems will arise from whether or not Arduino is smart enough to compile .S files, the timer interrupts, and also functions which disable interrupts.
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