So I ended up having to modify the clock design slightly.
In my program, along with a standard NOT gate, I also have a special dummy gate, which I call CONN, which is a simple passthrough. I needed this contruct in some occasions to connect 2 wires together. It is built simply like this by connecting 2 NOT gates:
I can get the delayed signal on the clkd wire. I also have a way to "pause" certain wires for a specific amount of time to simulate the actual delay. Basically this clock operates in "quarter ticks", and allows to simulate the bevaviour in the book. Here is an output from the test suite @ 1Hz, with "clock debug" turned on:



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