I have both engines out, swapped both upper and lower oil pans, swapped oil filter housing. Motor mounts. What do I do about the engine wire harness? Do I have to swap that too, I kept my ecu and traction control unit from the sc.

 

from my quick research the 96 SC engine is the same as a 1st gen LS400 engine so you will run into compatibility issues with the wiring harness.
If I am wrong and the engines are same, the connections from the donor engine should simply mate to the LS chassis wiring with no problems.

I never knew the differences in oil pans and oil filter housings between the engines (might only be due to chassis fitment differences) but this might also be an indicator of an older engine compared to the LS400.

 

You want all the Old engine that is the one that came with the car, you want all of its electronics on the new engine. All electrical to be keep the same as from the factory on the car. If the old engine is like a gen 1 then you will likely need that intake manifold and egr to put on the new engine. As well as the air meter unit from the old engine.