Errrr, couldn't you utilize: https://onion.io/store/arduino-dock-r2/ ?

It seems that you would then get the maximum response from your sonar, and then shuttle the data from the arduino chip one to the omega. For around $25 (20 for the dock, and around 4-5 for the sensor) you could get this done much in the same way you have before, without having to depend on linux timing being a bit inadequate for the task.