I've heard of at least 8 different ways to do this and they all work from what I've seen. I'm with you on this one Dustin and I'm going with the linear actuators as well. There are a couple of "out of the box" multi position controllers designed for use with the actuators that can make the job simpler. If you are wanting something closer to OEM, the actuators are used on the original. Since you are using a Arduino board, you can use a multitude of input sensors (GPS, temperature, magnetic pulse, light, water, contact etc). What type of 12 volt relay are you using for the actuators? Does the board treat the actuator as a servo and tracks position or uses the limit switches for full open and closed positions?
Thanks,
Chris