I went through the step by step process on setting up a vex net connection to control the cortex via. joystick, however after i go through all of the processes, the vexnet light indicator rapidly blinks yellowish color. any help?/ideas?

The rapidly blinking yellow VEXNet light means that the two devices are searching for one another; I would suggest plugging the Cortex into the Joystick via the USB A-to-A cable and turning both on at the same time; this will mate the two together. Then, when you wish to connect the two, make sure you turn both the Joystick Controller and the Cortex on at roughly the same time, which should allow the two to find each other easier.

On a side note, we have a very nice setup guide on our wiki you may want to check out, and VEX also has a Cortex guide PDF (including the ever-useful VEXNet LED code chart) on their site.