As a physics student, I wonder if there is a way to tell if the universe has been "tampered" with.
There is. A person is working on it now. The gist of it is to know the parameters -- laws of physics -- that nature cannot escape abiding. Look for an anomaly that occurs outside the laws of nature.
An analogous example: a distant cousin to us Earthlings using a highly advanced telescope were to look at Earth and were to see the Hover dam that caused the Colorado river to back up to form Lake Mead they would know they were locking at an other than nature created structure. They'd naturally assume that it was created by conscious beings.
That method applies to viewing the cosmos. Search for cosmic events that fall outside nature's law.
Interestingly, evidence or proof may be sitting in the humongous mountains of data already stored on computers. It would require a massive effort to sift through that data and require asking different questions about it. A much quicker method is to create overlay charts.
See DemocRATS? No need to be all pouty. Surely you will win an election by then!
The thing is, we wouldn't know what an untampered-with universe would look like, so the trick is to formulate the laws of nature without being able to see the universe "in the raw."
Therein likes the trickiness. :)
If someone is engineering the universe, it will likely involve the maniupulation of fundamental physical quantities over vast scales, so that to we uneduacted hicks on Earth, it will look like it's supposed to be that way.