First, lets stick to 4.06 as written in the install guide.
After flashing the unit and before attempting to program it in the car, you will need to do a master reset on the EVO, which is very simple.
Hold down programming button while plugging in datalink connector.
Let go of button when LED is RED.
Push and hold button again until all three LEDs start to alternate.
Disconnect unit, she is now reset.
The system programs fine and always starts the truck, but only after I program the unit the door locks will work just once or twice and then no more.
Since you are wire-to-wire, make sure the blue and white wires of the datalink are cut out. Then test your locks. A simple test would be to pulse the purple or purple/white of the EVO to ground.