Have you considered the pixhawk system? It's fully open source and runs the ardupilot firmware. I know the fixed wing software actually has a wind estimator included to ensure the uav tracks the correct patch over the ground so you might want to look into that. Also any of the arducopter systems are able to record datalogs, and you can record both the raw sensor data and also the calculated airspeed.
There are two options for differential airspeed sensors, an analogue one, and a more precise but expensive digital one.
Ardupilot has a fairly well written kalman filter and doesn't have any major gyro/compass drift issues as they are constantly compensated for but I don't know the exact stats. Some ardupilot powered UAVs can fly several hours with no issues.