CubeSat systems have the potential to make significant contributions to multiple areas of astrophysics research, including detection of gravitational wave counterparts, Gamma Ray Bursts (GRBs) and GRB afterglow, X-ray and ultraviolet astrophysics, exoplanet studies, solar, ionospheric and space physics, and variable star astrophysics including pulsar detection, Active Galactic Nuclei (AGN) physics, transient, time domain, and multi-messenger astrophysics. Several of these areas of astrophysical research utilize the radio frequency (RF) spectrum between 10 MHz and 10 GHz. This spectrum accounts for significant opportunities for research with space-based CubeSat systems and networks. While other frequency ranges such as millimeter-wave bands are important for research, the 10 MHz to 10 GHz frequency bands are optimum for CubeSat applications. Given this wide frequency range, the question becomes how to incorporate this capability in small form factor CubeSats. Swarms or constellations of CubeSats can be configured to perform multi-aperture Very Long Baseline Interferometry (VLBI), which is a fundamental technique for radio astronomy. The applications of CubeSats for detection of radio frequency counterparts of high energy phenomena with VLBI will be the focus of this study. This study is divided into two sections. Section 1 is a high level overview of the basic concepts, architectures, and technologies of a CubeSat system utilized for radio frequency counterparts of high energy astrophysical phenomena. This section was independently published in the Journal of the Society of Amateur Radio Astronomers (JSARA) and can be used as a standalone document for introduction to the subject discussed herein. Section 2 is the detailed analysis and design of the specific topics introduced in Section 1.