I just finished putting in the trd short shfter (awesome Mod) and next to the shifter I found 2 unattached hookups....

What are they

they arent for the Ipod or Aux since those are hook up already

 

Probably wiring harness connectors for the auto shifter illumination etc.

 

that sounds right.

I wonder if I can use those to hook up some lighting

 

The connector for auto shifter illumination has Green wire (power from the taillight switch) and White/Green (regulated ground from the dimmer). So you can use Green as you positive source, but its better not to tap anything into W/Green, just get ground from any metal part of the chassis.