Manufacturers are facing increasing pressure to reduce the development costs and deployment times for automated assembly systems. This is especially true for a variety of precision mechatronic products. To meet new and changing market needs, the difficulties of integrating their systems must be significantly reduced. Since 1994, the Microdynamic Systems Laboratory at Carnegie Mellon University has been developing an automation framework, called Agile Assembly Architecture (AAA). Additionally to the concept, a prototype instantiation, in the form of a modular tabletop precision assembly system termed Minifactory, has been developed. The platform, provided by the Minifactory and AAA, is able to support and integrate various precision manufacturing processes. These are needed to assemble a large variety of small mechatronic products. In this thesis various enhancements for a second generation agent-based micro assembly system are designed, implemented, tested and improved. The project includes devising methods for tray feeding of precision high-value parts, micro fastening techniques and additional work on visual- and force-servoing. To help achieving these functions, modular and reconfigurable robot end-effectors for handling millimeter sized parts have been designed and built for the existing robotic agents. New concepts for robot end effectors to grasp and release tiny parts, including image processing and intelligent control software, were required and needed to be implemented in the prototype setup. These concepts need to distinguish themselves largely from traditional handling paradigms, in order to solve problems introduced by electrostatic and surface tension forces, that are dominant in manipulating parts that are millimeter and less in size. In order to have a modular system, the factory the main part of this project was the initialization and auto calibration of the different agents. The main focus, of this research, is on improving the design, deployment and reconfiguration capabilities of automated assembly systems for precision mechatronic products. This helps to shorten the development process as well as the assembly of factory systems.  A strategic application for this approach is the automated assembly of small sensors, actuators, medical devices and chip-scale atomic systems such as atomic clocks, magnetometers and gyroscopes.