We apply a novel pre-flare tracking of sunspot groups towards improving the estimation of flare onset time by focusing on the evolution of the 3D magnetic field construction of AR 11429. The 3D magnetic structure is based on potential field extrapolation encompassing a vertical range from the photosphere through the chromosphere and transition region into the low corona. The basis of our proxy measure of activity prediction is the so-called weighted horizontal gradient of magnetic field (WGM) defined between spots of opposite polarities close to the polarity inversion line of an active region. The temporal variation of the distance of the barycenter of the opposite polarities is also found to possess potentially important diagnostic information about the flare onset time estimation as function of height similar to its counterpart introduced initially in an application at the photosphere only in Korsós et al. (2015). We apply the photospheric pre-flare behavioural patterns of sunspot groups to the evolution of their associated 3D-constructed AR 11429 as function of height. We found that at a certain height in the lower solar atmosphere the onset time may be estimated much earlier than at the photosphere or at any other heights. Therefore, we present a tool and recipe that may potentially identify the optimum height for flare prognostic in the solar atmosphere allowing to improve our flare prediction capability and capacity.