I hope this will help anyone else out that might be have similar issues as I. But after another few more hours of thinking and tinkering I was able to get my set up to work. However, it by no means uses the pre-programmed profiles. I had to make one.
Here is what I did.
1. Download the "Aura config tool" a simple search will pull up the right site with the download and set it up per the website instructions ( the setup wizard for programming the aura boards will make this much easier and it's what I reference).
2. Make a new configuration with the transmitter type as "Spektrum", receiver connection as "spektrum remote".
3. Connect the aura 5 board to your computer via the USB cable, and click connect in the program (should be in the bottom right of the window)
4. Hit the "Write All" button near the bottom right of the window.
5. Disconnect the Aura from the cable.
6. Boot up the flight-controller as you would with any other Spektrum receiver (by holding the BIND button well plugging in the battery [this will be easier with a second person])
After doing this the controller and most importantly the satellite receiver went into bind mode. once its in bind mode boot your transmitter in its bind mode and it should bind! For the most part after this I followed the basic setup as per the Flite Test video to make sure the gyros were working in the right direction.
I did come across one more strange thing though. After binding and getting everything set up I noticed the gyro assist was working in the proper direction for the elevator but my inputs were reversed! Reversing the servo in the controller will NOT fix this you have to do it via the config tool if you have this issue.
1. Go to the servo ports tab in the Config tool program
2. Select servo port 4 (this is the default for elevator you may need to do this with a different port if its happening with rudder or aileron)
3. Scroll down to the servo port output tuning section
4. Change the direction from "normal" to "reverse"
5. Connect the aura 5 to your computer as before
6. Click the "Write all button again"
After this the gyro should move the control surface in the right direction and the transmitter input was in the right direction.
NOTE you can do all the set up (except for Binding) well the plane is on and connected to your transmitter and/or in the basic setup mode as per the video to test everything before disconnecting the aura 5 from your computer. This can save some time and speed up the process.
Also be sure to save any configuration changes you make! The program does NOT auto save.
One down side to doing this though is that most of the gains for the gyros will be default and NOT the same as the pre-programmed configuration. You may have to play with those to get them working how you want. This does require flying then re-hooking it up to your computer. This can be a lengthy process.
Personally I think the aura configs tool's set up wizard is very strait forward to use and easy to learn if you just poke around a little. This can make other setups that are not pre-programmed like differential thrust much easier to do.