I don't know about the Ardupilot software but its worth having a look at - there are various IMU frameworks out there I believe.
As for a small board - Pro Mini (can even go to 3V3 with the 8MHz version, reducing parts count if IMU is 3V3). However motor driver is likely to want more volts anyway - stacking a standard motor shield on an Uno is simple at least. There may be a simple IMU shield out there too. For miniaturization have a look at www.pololu.com, probably have some small motor controllers.