Need Assist with Hacking - Shell Script

Well hello guys,

I successfully uploaded a shell (Antichat script) to my university's website. Website however required login to upload and I provided credentials of my classmate to login and all was ok. I accessed shell but now what? I was just not expecting it to be that vulnerable so I was not prepared or did any research. I browsed some files and sensitive files gave me permission denied error. I went off after some time because I was using my REAL IP!. Today the script is deleted, but I can probably upload it again I think with Tor but I think they will again know what my IP is because steps will be similar. Now I want to know how they knew my script's presence? Anyway to stay hidden and how to get access to files which give me error. And last question that I am at any risk because I was on real IP? What could be consequences for just browsing their server files? (Will stay careful next time pals)

Thank you!