Alvaro -
This is really a good design. It avoids the timing problems of using a serial packet to trigger the acquisition. The FTDI USB/Serial driver has issues with buffering on the chip side (384 bytes), the driver side (64-4K bytes) and when the buffers are flushed to the application ( 1 msec polled).
Could you describe the serial protocol a little bit more ? So I can try to interface your Arduino code with a PC Processing oscope program.
Keep up the good work !!