So I'm in the process of wiring up my s4 na shell with an s5 turbo harness. I looked at the fuse box for the s5 turbo inside the car and I believe they are different compared to the s4 na. The pigtail that connects to the fuse box are different.

To save time on my part, I was wondering if I can cut the harness that goes to the fuse box leading to the rear hatch where the lights and such are, and swap it with the s5 turbo pigtails?

 

you are making it more difficult than you need to be.
I put a S5 TII engine in a S4 N/A chassis and didn't change squat at the rear harness.

If you are using the S5 TII engine harness then I can see a little difficulty if you do not know what you are doing.
I got rid of all the engine crap that I did not need and ran the Engine with just the basics.(sensors and fuel injectors,etc) like a Regular S4 engine..I used the s4 N/A harness to the engine.
The S5 OMP gets ditched and you can either go with a S4 OMP setup and front cover or Premix your fuel)

 

I guess I did it the hard way. I ended up using the s5 rear harnesses as well because the plugs are different on my fuse box. Got it all hooked up now so I'm just glad I got it over with. Yes, it was time consuming and difficult.