Changing the MN3007 won't affect the clock frequency. If the BBD was loading the clock in some way, what you'd hear would be degraded signal through the BBD as the clock pulses get rounded by the loading, and in the worst case it wouldn't pass signal.
If the clock frequency is too low, the first place to start is the VCO capacitor, C29/39p. 39p is actually a really tiny value, so it's just about possible you could have stray capacitance affecting things. I'd certainly make sure to clean up the board well around the clock. If any of the clock's tracks on that Sabrotone layout are longer than they need to be, I'd shorten them too. Parallel tracks on a stripboard have measurable capacitance, and it can be ten's of pF, so it'd hit us for this job.
After that, you'd have to work backwards through the 4007 into the range-setting components (IC3c, IC3d, IC2a) and make sure everything is as it should be there. Could be as simple as a wrong value in that part.
I'm assuming that calibration of the range is done with the Manual control and the LFO not playing a part.
HTH,
Tom