Self-assembly, trapping, and transport of microparticles can be pivotal in medicine, lab-on-a-chip applications, and other fields; however, complex non-Newtonian fluids pose fundamental challenges for these processes. Here, we show that for two glass boundaries set amongst a viscous, shear-thinning gel and separated by a narrow slit (~20 µm), incident acoustic waves are concentrated at the interstice, and microbubbles in the surrounding gel exhibit consequent nucleation and other interesting behaviours. When the acoustic field is intermittently activated, microbubbles transform between spherical (off) and ellipsoidal (on) shapes; ellipsoidal microbubbles squeeze into the interstice and become trapped, while spherical ones are pushed out. Upon continuous activation, the ellipsoidal microbubbles execute propulsion driven by Faraday waves superimposed on volume modes developed at their surfaces. When in proximity, they self-assemble into a chain-like microtrain capable of trapping microparticles between its members. Upon deactivation, the microparticles are released, thus simulating a microcargo train.