Nolan

MSP Flasher (rather than CCS or Energia) is the best way to sort out any firmware issues. It shows you what firmware you have and lets you quickly and easily update it. If you suspect the firmware does need updating then that's the tool to check/fix it for you. Whilst the IDE may do the firmware update I've found they can be a little flaky on this.
http://www.ti.com/tool/msp430-flasher
 
As far as Energia goes, I stay well clear of it so can't help you there.

Just run mspflasher.exe from the command line (in the MSP430Flasher_1.3.3 folder). It should tell you what FET and MSP430 is connected and let you upgrade the FET. It's also used for flashing firmware - hence the name.

Success!!! I am now back tracking to find out which of the things worked since i foolishly tried multiple things at once.
 
I am now able to (using your code from above) see the text numbers appearing in the Energia COM5 serial monitor without needing puTTY. 
 
Once I figure this out, do you mind if i type a summary of what we tried so that others in the same situation can run through the steps faster? It would of course include a link back to this blog and give full credit to you for all of the ideas. 
 
Thank you for your time. I will definitely be using this blog site in the future for more help. 

Energia runs the FR5969 at 8MHz to avoid employing FRAM wait states (kinda silly IMO as they don't seem to hurt much). But the fact is the FR5969 has TWO hardware UARTs. I recommend you use them.
 
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