I have got the board of Prototype 3a back from the fab and populated it and uploaded the code. Most functionality is working.
1) Current limiting on negative rail does not work. There was an error in the Schematic
2) The Positive rail only goes down to 0.62V when there is No load. This is because the LT3081 Requires a 5mA Load for line regulation.
Prototype 3b: Revision Concept Includes DAC Output, 2X Analog Inputs(0-12V) and 4x Digital Inputs 3.3V (5V Tolerant)