It seems to me that calibrating the clock is the least of the problems here - the whole system is going to be one big unknown and unless the whole thing is calibrated there seems little point worrying about whether one component is accurate to better than a few percent. (How accurate are the torque measurements going to be? How accurately do we know the inertia of the mass? What are the effects of friction, air drag etc? How accurately can we measure RPM and roadspeed given that they are varying continually?)
Since the dyno isn't going to provide enough data to correct the readings to standard conditions the accuracy is going to vary day by day, even if it was properly calibrated in the first place.
This dyno will be useful for doing back-to-back comparisons but I don't expect it to produce figures that are meaningfull in absolute terms.