Somatic embryos are bipolar in nature and from single cell origin. If only rhizogenesis happen, you have to try different PGR concentrations and combinations for embryogenic callus formation. Mostly auxin (2,4-D or NAA) followed by blank or low concentration of auxin will helpful in somatic embryo induction. It is also highly depending on the nature of the crop and genotypes within that crop species.
Since your objective is to induce somatic embryogenesis.the roots ate of mo use. The somatic embryos are bipolar and the will form both shoots and roots. Having said that I would advice that you reduce the ammont (concentration ) of auxin in the media. You could also try using cytokinins alone. I have developed a protocol for Coffea arabica using cytokinins alone. TDZ is very good.
The trend of differentiation could be affected by the ratio of the exogenously supplied growth regulators auxin and cytokinin. So, in this case, auxin is inappropriate for induction stage. Also,as was mentioned above, adding BA or /and kinetin in medium is useful for somatic embryos formation with reduce or omit the auxin from the medium to allow somatic embryo development to progress.
This paper maybe helps; www.publish.csiro.au/journals/spjnas
The south pacific journal and applied science, 28,27-40, 2010
Since you only desire somatic embryos, I would support Jane Wanjiku Kahia by suggesting use of TDZ, which is a highly potent cytokinin for woody plant species. I have used TDZ only to induce somatic embryos and recover plants from zygotic embryos and cotyledons of the tree Melia volkensii.
Try to use BAP, Kin & IAA, NAA, 2,4-D ratio, because i am also getting very good results with these combination.
As per my observation , those callus, which is producing roots, are generally not producing embryos. so generally i m discarding those callus.
Take some tips and suggestion from Barbara M. Reed for your work. (https://www.researchgate.net/profile/Barbara_M_Reed), she did very good work on pyrus micropropagation and related crops.