After doing a little bit of research it turns out that the Yun does not have its SPI pins broken out to the digital I/O pins as they are on the Uno and instead are only connected to the ICSP connector. So no wonder it wasn’t working. After hooking up two modules to two Uno’s they were able to communicate to each other successfully.
I have no idea why the ISP pins are not broken out on the Yun like they are on the previous Arduinos but i’m sure there is a valid reason for it.
So, now I have two device communicating the next stage in this project is to hook up some sensors to one of the device and have it sending the data back to the base station device. After that, the circuit will be powered by battery and using sleep modes will sleep in-between sending data to conserve energy.