So I have an 88 N/A shell with an S5 headlight harness. I'm planning on swapping in a JDM S5 TII motor in the future. Would I just need to get the JDM harness or both the JDM and USDM harnesses in order to make it work?

 

If the headlights worked with that switch setup before you yanked the engine then it is not applicable to what you are doing now.(engine swap)
The Engine would be Better with a USDM harness and US ECU.
The JDM harness is on the right side and the US harness is on the left so it would Fit better for one thing.
The thing though is that you are putting an S5 Engine into an S4 and that would entail a bit of wiring.
If you can get the Engine to Operate,component wise as an S4 then you would be OK.You could use your S4 N/A harness and just extend a wire or 2..Use the S4 AFM,boost sensor,etc and the engine would be running in no time.
If you put a Stand alone ECU on the engine that would fix Everything.
I'd drop the Electric OMP though and premix.That Part makes me want to kill puppies.

 

The thing is I bought it as a shell so I don't know if it was working or not when the engine was in there, and I have neither s4 or s5 harness. I was also missing the emissions harness. So I presume it's better to just get s5 everything then, sort of like running a full s5 conversion in an s4 shell. I am still learning wiring diagrams and what not, and as I type this I'm currently wiring the other half of the headlight harness that was cut off lol. I am in the process of sourcing an s5 dashboard harness as well.