Assuming I understand you, you are saying that the units have the same BPM but are not synchronized to the beat.
I suspect this is inevitable – MIDIclock does not have a beat indication (it's essentially a stream of pulses) so there is no way to do this. There might be some way we could use the MIDI start command, but this only really makes sense in a sequencer/sampler environment.
Maybe we'll get some ideas (or someone out there can help), but I don't see a solution here. One could perhaps use MIDI time code or such, but this would be getting excessive for what is after all a guitar pedal