I installed a remote starter in my manual trans JK back in January. I was a bit uneasy every time I started it, I would usually look out of my window to make sure it wasn't driving away. So, I used some components to rig a neutral safety switch.
This circuit will prevent the remote starter from working when the Jeep is in gear. I can still disable the remote starter with a switch as well. I also included a LED because I like things that light up, and so I can be sure it's working.
The only thing I had to buy was some magnetic reed switches, these are essentially those magnetic sensors that you see on doors for security systems. It is important that you get ones that operate as normally closed. This means normally the circuit is connected, but when a magnet gets close to the switch it breaks the circuit.
I failed to take a picture when I had the center console off, but I just my MS paint skills to make a pretty picture. In the picture you can see I secured the magnetic switches around the shifter with a big circular clamp that is usually used for attaching a dryer hose. I then attached magnets to the shifter with epoxy and smaller hose clamps(not pictured).
Here are some videos of it working: