Mike’s comment on my previous post:
It may be useful, instead of oscillating the input to the encoder, to have the mote toggle the input to the encoder. This should cause a code to be sent once and received, which will then cause the corresponding pin on the decoder to toggle. The mote can then verify this toggle to indicate that the beam is uninterrupted. The mote can run this routine every 5ms or so. Two or three failed transmissions in a row could be considered as an activation, and the mote could then broadcast it’s “my beams been broken” signal.
This seems like a good idea, but we must also account for a 27ms delay between when a pin on the encoder is toggled, and the corresponding changed is noticed on the decoder. Here is a screen from the oscilloscope:

The output from the pin on the decoder is on top, and the toggle for the encoder is on bottom. An oscillating toggle was used so we could view this delay on the scope. Notice the 27ms gap, shown by the cursors, between when the encoder is toggled again from being off, and the change in the decoder pin.
To be clear, a “broken signal” in Mike’s comment means there is no change in the output of the pin on the decoder. Notice on the scope, it only changes when the LED is on, goes off again, and then comes back on. If the second on, in this example is interrupted, and the LED goes off before the signal reaches the transceiver, the decoder pin will not change.
Here is a picture of the current circuit, as it is wired. For testing, I plan to put both on the same board.
