I was under my car trying to isolate some noises when I happened to notice something that looked like it might not be right. I had the dealership install the TRD short shift kit when I bought the car... and where one of the shift cables turns up towards the new cable bracket, there's a wire clip-thingy. It looks to me like it should be under this clip... Does this look right?

 

Couldn't say for sure... but I would guess you're right. especially with what looks like the exhaust right there.