I am working through the exact same thing right now!
My build modified the 'Cepheid' to a 'Cesar'. I finished it a week ago and it was distorted with the Blend on '0' (no effect) and then it quickly went silent as I blended in the effect. My LFO LED was blinking and reacting appropriately to the rate control.
I was using 18vDC power supply (which loaded and trimmed by D100 - 1N5817 diode, the Vcc = 17.5) and used a 15v Zener for D101, which in practice only regulated the Vcc B down to 16v and Vref B to 8V. Accordingly, I swapped D101 for a 13v Zener and am getting 14v, which is where MN3007 and MN3101 are supposed to operate well (they can take 18v max before damage).
I socketed all my ICs and transistors and am expecting to get to loading just IC 2 and the transistors, to see if the dry side is working right. If successful, I will load IC 3 & IC 4 to see if signal will pass (it should without the LFO, IC 1, wiggling it).
I am hoping it works as these chips are NOS that I purchased in the 80's, left over from a Roland JC120 restore. I am wonder if
@Robert knows if this BBD + Clock chipset was ever verified with this PCB? In comparison to the original Boss CE2, it should. The only difference I found is that for the MN3007 CE2, Pin 1 is ground and Pin 5 is -15v, where the Cepheid has Pin 1 at +15 and Pin 5 to ground, which is electrically the same thing.
Let me know if you figure it out and I will keep you posted on my progress.