Your problem should not be related to your mods. Even if they wanted to hassle you they would have to prove the mods caused the problems.
If your intake is easy to swap I would put the stock back on but I wouldn't worry about the exhaust.

 

I doubt you'd have problems with the exhaust, if you are really consuming oil then it's an internal problem. There is no way you can cause an engine to consume oil by putting a different exhaust on it.

Intake on the other hand, they could try to argue that the filter is not good enough and it let some particles or something into the engine, which caused the oil to leak into the combustion chamber. I know that's bullsh1t reasoning but I'm just trying to think like a stealership.

 

I'll probably switch it out for a while then... damn....