It has been a while since I read smt, I used to have a cheat pdf with common values. I thought 103 was 1K but it is actually 10k, anyway 503 would be safer to use , that's 50Kohms for the pulldowns.
the led detector might work at that 1300 ohm value but to be safe, I would use 10k, or 1002 in surface mount code, which is the same as in the intellimouse circuit diagram.
edited because i confused the detector in the schematic
I did a similar project before with a teensy 2.0 except I couldn't stop the wheel detectors from dying through overcurrent, even with series resistors to protect the detector(In your schematic there are no series resistors). According to the datasheet once 4ma is exceeded the wheel detectors get shorted and die quickly. So although I have the most experience in this thread I still am none the wiser. In theory duplicating the pcb exactly should work, but one major problem is you don't know exactly what detector is used. I wrote about my failures here:
Maybe the mcu zowie uses only sinks 2ma per pin, compared to the teensy 2.0's 40ma, if that were the case there would be no problem. I will leave it up to you to find zowies mcu datasheet.
You should prototype the circuit on some stripboard or by freehand even to test it before ordering a pcb, to keep cost down.
you used the symbol for photo detector for the led in your schematic, that must be fixed. emitter A should have a 10K resistor in series, before the pulldown, same as the intellimouse schematic. Then do the same for emitter B
edit, found the datasheet for the 3310 zowies, mcu pullups are 5.6k, I guess that's why it is rare for zowies to develop doubleclick. i/o pin current ranges from -25ma to 50ma max, so somewhat similar to the teensy 2.0