@Gavin Grant This isn't quite what I was looking for, as I was trying to get execution synchronized with wall clock time. I realized the problem has to the fact that I am trying to acquire signals in real time and to do this I need to be using Simulink Desktop Real-Time blocks. I have update the model to use Packet Input blocks rather than UDP Receive blocks. After adding those and a Real-Time Sync block, I can use the desktop real-time app to 'Run in Real-Time' and it seems to execute with the correct timing.
Do you know if those desktop real-time blocks can be used with Simulink Coder to generate an executable? I eventually want to run this model as a separate process using an executable. Thanks.