Quick situation background - 1998 4runner limited with port/dealer added RS3000. I've done a ton of research just to get a fob programmed and working. I have the TSB on how to program it as well as an RS3000 manual I found online. I have a grey 2 button factory remote as the TSB describes for 1998.

With the key on and the programming button depressed for 3 seconds, the Toyota Security LED doesn't ever illuminate as it should so I can sync the fob. Looking at as much wiring as I can see with the left kick panel off, everything seems intact. The only non-stock item is the radio. Does the RS3000 system interface with the factory radio at all?

Also, what is this for? It has a button on the back that will illuminate the LED. I believe it's connected to the blue glass breakage sensor.