Well, the main difference between Duemilanove and Uno is the USB interface, so it's not surprising that a serial interface doesn't continue to act in the same way. http://arduino.cc/en/Main/Boards I wouldn't expect the same results from the USB interface. Duemilanove boards are still available (and being discounted) so you should try to get some.
It's just my opinion, but I would start this project without the MIDI implementation. Start with the basics. First, I would start with the basic "blink" example, combined with the "DigitalReadSerial" example. Using three buttons and three LED's (and the necessary resistors), printing the values to the serial port, you can simulate almost totally what you want to do with pedals. You will print the note number to the serial port for each button press, for example, without the complications involved in sending MIDI data. That way, you know the basic logic works, and you have very simple wiring, and can see what it does (easy to debug, get help, ask questions, etc.). After you have the button presses lighting the correct LED's and incrementing/decrementing the values, and printing them to the serial port, it will be relatively easy to change the serial "prints" to MIDI "prints".
Has anything happened recently in this thread? I am looking for almost exactly the same thing. Only my MIDI player will actuate relays that "play" strings of Christmas lights corresponding to MIDI note values (only 8 of them). Using the sparkfun MIDI breakout shield, the K74 relay kit, and the MIDI Glockenspiel code from Mike Cook http://www.thebox.myzen.co.uk/Hardware/Glockenspiel.html I can now "play" lights using a MIDI keyboard. My last goal is to read in a MIDI file and have the Arduino repeat the sequence over and over. Is this worth a new thread?