I had a similar problem and came across your post here. The solution for me was to connect my two DC motors to ports 3 & 4 of the Adafruit motor shield (v1). I'm also using the IR remote library by Ken Shirriff and in IRremoteInt.h he states:
// Uncomment the timer you wish to use on your board. If you
// are using another library which uses timer2, you have options
// to switch IRremote to use a different timer.
#define IR_USE_TIMER2 // tx = pin 3
It appears that on the Uno the PWM timer on digital pin # 3 is being used by the IRremote library as well as the motor shield (when you activate DC Motor #2 or Stepper #1 http://learn.adafruit.com/adafruit-motor-shield/faq
If you found another solution please let me know.
BTW you are thinking along the correct lines by connecting the data line from the IR receiver to pin #2 because digital pin 11 is used by the motor shield when you activate DC Motor #1 or Stepper #1.