Hey guys,
This first picture is with the alignment tool off, and the shifter slightly tilted toward the driver side, the threaded cable end falls in to the threaded groove without issues.
http://i51.tinypic.com/a4vqsx.jpg
This second picture is with the alignment tool on, so the shifter should be perfectly neutral. The cable is not long enough and the threaded cable end does not fit completely into the groves. Most of it would fit, but the will be about two threads sitting on top of the non grooved parts.
http://i55.tinypic.com/2eevkux.jpg
Thanks for all your help guys.