as i got into bigger and bigger rocks my atrac just couldnt help enough (a lot of stop and start on obsticles and what not), so i bought a used elocker from a 96 runner on ebay for 330 bucks. had it rebuilt and installed it with a 12vguy harness. the difference is night and day vs just Atrac. honestly modifying the housing wasnt too bad. just 2days with a dremel and a good drill was all it took. and i love it. however the actuator does take some maintenance to keep it 100%, but being a EE student helps with understanding what the issues could be and how to address them, so its not a big deal to me either.
Since you're an EE you can maybe appreciate this theory. One of the issues I've read about when setting up control of the Toytota elocker with aftermarket wiring and relays, etc., is that the motor tends to jam at the ends its travel. The common solution to that is to put resistors in series to slow down the motor so it doesn't run into the stops as hard.
I've often suspected that's not the proper solution. I would suggest instead using a SPDT relay for each direction, and when the limit switch trips, wire the relay to open the connection from +12V to the high side of the coil, and at the same time short the high side of the coil to ground, which will put short across the coil. Putting a dead short across a permanent magnet DC motor will stop the motor immediately, so it won't run into the stops and jam. That way you can dispense with the resistor and run full power during actuation.
Not sure if you've had those issues, but something to consider. It might require a couple of DPDT relays to wire it to do that and still operate in both directions, but I'm sure it can be done. I strongly suspect that's what the Toyota controller does, or something similar.