New to programming, trying to accomplish the following

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But how can you trust something you already know has problems?, by doing it properly you overcome those limitations.
 

Is this because the MCU itself doesn't have a reliable enough internal clock for such a timing sensitive situation?
 
Is this because the MCU itself doesn't have a reliable enough internal clock for such a timing sensitive situation?

No, the internal clock is perfectly fine, it's (as I've said repeatedly) that the link doesn't accurately maintain the width of the pulses.
 
You could also try 40KHz transducers, put the RX on the one board and TX on the other. You will need an op-amp circuit on the reciever side, but that will also help to set the sensitivity.
 
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