Building on our previous work on transient, two dimensional simulations of the Navier-Stokes equations to investigate mixing enhancement by introducing the Lorentz force in MHD as a control parameter to create turbulentlike chaotic advection, this paper describes transient, three-dimensional simulations. Our approach differs from many previous analytical investigations by other workers based on potential flow and linearized stokes flow. A shallow disk-ring cylindrical microfluidic cell with gold electrodes deposited on the floor serves as a representative lab-on-a-chip. By applying a voltage across specific disk electrodes and a ring counter electrode, a current is established in the weak conductive solution. The current interacts with an externally applied magnetic field generating a Lorentz force that causes fluid motion. Velocity vectors, electric potential distributions and ionic current lines are presented. By switching on and off a pair of disk electrodes with a certain period T, a "blinking vortex" that induces chaotic advection is produced. Various particle trajectory-based analyses using extensive postprocessing of the simulation results show that the period T plays an important role in generating chaotic advection. Large periods provide efficient stirring which improves mixing performance. Taking a step further, we show that by having two pairs of disk electrodes that were subjected to a different on/off switching scheme, more complex chaotic motion can be generated, and the mixing region can be extended to almost the entire fluid domain. This study establishes CFD simulation of MHD at the microscale as a robust tool to develop efficient strategies for mixing by chaotic advection. The techniques developed in the present work are also applicable in MHD-based flow control in microfluidics for other applications such as pumping and steering fluid to target locations.