Thanks for all the ideas. I am a few new projects in the list now.
Couple answers to questions.
1. The key that's missing now was a key without the buttons on it. Not sure if it had a chip / RFID / etc in it or not. It was not a Toyota key, it was some kind of copy. It was what I used as a valet key and kept hidden (obviously not well) in the center console. It was definitely how they got it started because although they pulled off the kick panel and fiddled with some wires, none were cut.
2. They got in because I leave it unlocked a lot. Ok I realize the combination of unlocked with the key in it, is probably not the best idea. Who knew? We've had quite a few break ins in our neighborhood over the last couple of years, and I often leave it unlocked to avoid unnecessary damage to the truck from someone trying to get in. I learned while living in Africa that if you make it easy to get in and also leave nothing in it, you're likely better off than locked with nothing in it. Again, except for when you do a poor job of hiding your extra key. Shoot.
Techstream / ECU / Key Programming
Sounds interesting. Agree with you
@jLB about just doing it as a precaution. I am taking it to the shop for a quick once over of the wires they fiddled with, since we're driving 2000 miles next week and loose connections don't sound like a fun project for the side of the highway with three toddlers. I'll ask about them helping with this too.
Kill Switch
Also a good idea.
@LandCruiserPhil that is pretty close to how I've done it in the past. I also like allowing the starter to crank but not turn over, for a lot of reasons. Hopefully I can incorporate the clapper into that.
Drawer
And locking drawer for the back just moved up my list for the few pieces of gear I keep in it all the time. Going with one of the DIY versions some guys have posted for this.
Jeep
And I think I'll try to park my jeep behind it now. It's hard to start, even when the kill switch is off. Or just build a garage.