Air intake/misfire

Okay, so recently I did a flush on my heater core
system because it wasn't working properly. In the
process of this I broke off a box that sits on the
back of my air intake (my car is an 01 Mitsubishi
Eclipse spider ft). Anyways, I broke the box off the
intake, and I decided it didn't do a lot, (boy was I
wrong). I then glued a small piece of plastic over the
hole that the box created when I broke it off. My car
ran fine for a couple of minutes but when I took it to
town (about 5 miles away)  it started jerking and
rough idling. So I then took it to autozone to get it
tested and it came back with codes /P0300, P0141,
P1400. My dad told me that it had to be because of
the box, that it was the only thing we changed. So I
went to Walmart and bought some silicone, and put
the box back on the intake but I still have the codes
and my car still runs badly. I would really appreciate
any help. I'm lost. Thank you.