Added Better PWM Generation project (and swapped out base code into the crio-FPGA-control/Current Loop - NI 9505 (FPGA).vi.  Updated UI Main.vi to add the additional controls to the tabbed interface and enable them by default when control mode was enabled.  Check Loop Error.vi apparently needed to be upgraded to 2013 still.
Added in current sensor gain in addition to the pwm gain inside Current Loop - NI 9505 (FPGA).vi.  These are critical for converting to/from physical units.
It appears as though the code will need to be re-written in fixed point - I'm looking into a NI-SoftMotion example that supposedly has already done this.

E-mail from NI regarding this below:
 -------- Original Message --------
Subject: 	Re: (Reference#7405581) Phone Support E-Mail
Date: 	Wed, 9 Apr 2014 16:58:43 -0500
From: 	support@ni.com
Reply-To: 	support@ni.com
To: 	oberstar@engr.wisc.edu

Note: Your reference number is included in the subject field of this message. It is very important not to remove or modify this reference number, or your message may be returned to you.

Hello Erick,

This is Ian from the Applications Engineering department at National Instruments. After you have NI SoftMotion installed, you can find the example I was referring to by navigating to Help»Find Examples»Hardware Input and Output»Motion Control»NI SoftMotion»Device Specific»NI 9505. I'll go ahead and leave this service request open for another week, so if you do have any other questions concerning this issue, please reply to this email or call me at 866-275-6964 and enter your SR# (7405581). Have a great day!

Regards,

Ian Knox
Applications Engineer
National Instruments
http://www.ni.com/support