Hi:
I believe you have TWO projects here:
Project #1 : NE64 code to toggle pins or do ATD samples as commanded by a PC via Serial Port or Ethernet Port. Code should be in C or assembly.
You should be able to find example code for this in the Freescale website for the NE64, or if you have Processor Expert and CodeWarrior, they create very easy basic projects to do this.
Project #2 : VB.net application running in PC to send commands to the evaluation board via Serial Port or Ethernet Port.
For this, you might be better off searching a VB.net forum.
Regards,
Alex