1999 Honda Civic Mysterious hose.

I bought my car 4 months ago. I had it about 3 weeks and took it on the freeway for the first time. After exiting the freeway my check engine light came on and it began to sputter. I had the CEL checked and it came back with codes for misfires on all 4 cylinders, a random misfire, another misfiring code, a code for each O2 sensor, and a voltage code indicating a clog or air intake issue. I replaced all the sparkplugs and the air idle control. I was told that this would resolve the codes for the misfires and most likely the O2 sensors. When reconnecting the air intake pipe my dad and I noticed an additional hose that neither one of us remember disconnecting. We looked for over an hour to try to find where this hose connects to and found nothing. It has proven to be rather difficult to find a clear image and diagram of this intake pipe and where this hose is supposed to go. I was able to conclude that the hose was or an EGR but my car doesn't have one that we could see. We capped the hose and drove the car and the car wasn't able to shift out of 3rd gear into 4th. My questions are 1) is my 1999 Civic EX supposed to have that EGR valve? 2) Where else would that hose connect to? I have had 5 people look at my car and not a single person can figure it out.