Frankly speaking, bone regeneration can only be assed histologically, radiographically you can claim that bone fill (repair) has been achieved. As far as any bone formation maker is concerned, i doubt if it would really justify the results of your clinical research. Coz as we know, bone formation and resorption process is continuously going on, and the bone formation markers (if any) can always be detected any time. Even if you get higher values during healing after periodontal regenerative surgery, you cannot say that regeneration is occuring, because regeneration means PDL+cementum+bone. Assessing only bone formation will again focus only on repair which can be more easily detected radiographically. So your whole purpose of study would stand in doubt.
Actually, I am in complete agreement with Dr Agrawal in that bone formation and resorption are a continuous and coupled process. Nevertheless, salivary levels of sRANKL and OPG, more importantly assessing their ratios at different times might provide an insight into the healing. We now have really sensitive ELISA tests that can measure the levels of these substances in saliva upto a few picograms. Matrix Metalloproteinases especially MMP8 and 10 could also be looked into as potential candidates for determining the phase of tooth movement.