Hi Andrew,
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.
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Hold down programming button while plugging in datalink connector.
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Let go of button when LED is RED.
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Push and hold button again until all three LEDs start to alternate.
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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.