Okay, just checked pin 10 of U49, and I'm guessing this is what you mean by "noisy". Mind you, that's just me stopping the scope. Maybe things like this don't matter with a clock signal, but it certainly doesn't seem clean. I've confirmed this signal remains crappy looking on the CLK inputs for U29, U30, U31, and U32. Note that my channel 2 is my source signal. And while the optocoupler output is a positive going clock signal, U49's is negative going. Looks like it's a base 5V signal, that clocks at 1V. Second picture is the large gaps in the clock signal.
Indeed, C38 is missing. Guessing it must not be necessary.
The output of the AT1 for the clock signal, btw, has gaps. guessing whatever is generating the clock is being reset every X cycles. So it's not a steady lock signal, but goes for a bit, has a gap, goes a bit more, gap, etc. That what you see? =/
Also interestingly, the clock on U49 pin 10 (and AT1 input and output) shuts down in diagnostic mode (any N level). So it must be driving the MUX. Which I guess makes sense.