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Hi,
Even if your files are inside UWSim they are just sending messages to each other through ROS, so no simulation is involved (That is the reason why you are getting CPU time). Unfortunately, as you said, UWSim does not offer this kind of simulation capabilities at this moment.
So, depending on the precision required I would suggest to implement it yourself adding delays, missing packages... depending on the position of both AUV's. Adding a accoustic signal sim node that receives messages, keeps track of the vehicle's position and resends messages to the possible listeners, so each AUV should have a publisher and subscriber that will send/receive to the sim node.