I thought when I tuned out the VATS it wouldn't bother me anymore. But low and behold it still keeps me from starting my car. Why doesn't the tuning take care of it completely? Do I have to install the resistors on top of tuning it out?

 

Yes, you have to install a resistor for the key pellet if that is not working (or bypass the theft deterrent relay). Tuning only takes care of one part of what the VATS does (eliminates the need for the fuel enable signal from the VATS).