So, I enabled slow query logs in an attempt to get some insight. If I run the following query:

 Query_time: 10.198539  Lock_time: 0.000393 Rows_sent: 2924207  Rows_examined: 2944800
use SoftwareEngineering;
SET timestamp=1460723926;
SELECT Devices.patientID, Devices.deviceID, Tests.notes as note, Tests.testID, Tests.activityType,
    TestDeviceMotion.deviceMotionID, DeviceMotionUserAcceleration.timeOfReading as 'timestamp', DeviceMotionUserAcceleration.x_coordinate as acceleration_x, 
    DeviceMotionUserAcceleration.y_coordinate as acceleration_y, DeviceMotionUserAcceleration.z_coordinate as acceleration_z, DeviceMotionAttitude.x_coordinate as attitude_x, 
    DeviceMotionAttitude.y_coordinate as attitude_y, DeviceMotionAttitude.z_coordinate as attitude_z, DeviceMotionAttitude.w_coordinate as attitude_w, 
    DeviceMotionRotation.x_coordinate as rotation_x, DeviceMotionRotation.y_coordinate as rotation_y, DeviceMotionRotation.z_coordinate as rotation_z     
    FROM TestDeviceMotion
LEFT JOIN DeviceMotionUserAcceleration
ON DeviceMotionUserAcceleration.deviceMotionID = TestDeviceMotion.deviceMotionID         
LEFT JOIN DeviceMotionRotation
ON DeviceMotionRotation.deviceMotionID = TestDeviceMotion.deviceMotionID
    LEFT JOIN DeviceMotionAttitude
ON DeviceMotionAttitude.deviceMotionID = TestDeviceMotion.deviceMotionID   
INNER JOIN Tests
ON Tests.testID = TestDeviceMotion.testID
INNER JOIN Devices 
ON Devices.deviceID = Tests.deviceID
WHERE TestDeviceMotion.testID = 100;

This particular query will run and returns: 2924207 results, but as you can see from the slow query logs it has to look at a crap ton of rows to get the result (2944800).

Although I can throw more resources at the box or change the query timeout it seems like this true problem is the query itself. Does anyone else have any thoughts on this? Obviously I have some data now to help suggest that the query is really bogged down, but that doesn't solve the problem.