Looks like you'll be collecting about 3 bytes per millisecond. I think you may be able to transfer that over the serial port in real time if you wind the baud rate up, but with that approach you would be vulnerable to anything that stopped the receiver from handling the serial input promptly. It would be worth trying, anyway. If that doesn't work you'd need to buffer about 4500 bytes in total which is too much for a standard UNO but would fit easily into the 8KB of a Mega.
I would have thought you could use a voltage divider for each digital input too, as long as you remember to connect the grounds.