I checked the Mux ICs (10, 11, 12, 15, 16, 17) and I can see the negative going pulses on pin 1 in each case.
Turning my attention to the clock, I re-inserted the original ROM and checked pin 6 of IC 3. The clock frequency was 9.38 Mhz and is clearly coming from the VCO as I could adjust the frequency with RV1. Pin 11 of IC 7 was High (6 Low) and as expected given pin 11, no output on pin 10. Just for fun I adjusted the VCO to 16Mhz however, no change.
I will quickly check with the second IVC ROM before coding up a ROM as was suggested by Neal, e.g.
Code:
ld hl, 0xc000 ; status write
ld a, 0x02 ; crystal dot clock
ld (hl), a ; write
loop: jr loop
This should give me something concrete to work with.